4,509 research outputs found
Partly melted DNA conformations obtained with a probability peak finding method
Peaks in the probabilities of loops or bubbles, helical segments, and
unzipping ends in melting DNA are found in this article using a peak finding
method that maps the hierarchical structure of certain energy landscapes. The
peaks indicate the alternative conformations that coexist in equilibrium and
the range of their fluctuations. This yields a representation of the
conformational ensemble at a given temperature, which is illustrated in a
single diagram called a stitch profile. This article describes the methodology
and discusses stitch profiles vs. the ordinary probability profiles using the
phage lambda genome as an example.Comment: 11 pages, 9 figures; v3: major changes; v4: applications sectio
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Impact vesiculation â a new trigger for volcanic bubble growth and degassing
We highlight a potentially important trigger for bubble growth and degassing in volcanic bombs. We have successfully triggered bubble growth in previously unvesiculated samples of silicate melt during experiments to simulate volcanic bomb impact, by firing pellets at, and dropping weights onto, melt samples. We call this phenomenon "impact vesiculation". Further work is required on real volcanic bombs to establish the extent to which impact vesiculation occurs in nature. However, our experiments are sufficient to demonstrate that impact vesiculation is a viable processes and should be borne in mind in analysis of bubble populations and degassing histories of bombs and spatter-fed lava flows. Degassing caused by impact vesiculation can occur only at ground-level, so any attempt to calculate the amount of erupted gas available for transport high into the atmosphere by convection above the source of a fountain-fed lava flow that is based on subtracting the volatile content of fluid inclusions from the volatile content of the resulting lava flow would be an overestimate if significant impact vesiculation has occurred
Tensor Rank, Invariants, Inequalities, and Applications
Though algebraic geometry over is often used to describe the
closure of the tensors of a given size and complex rank, this variety includes
tensors of both smaller and larger rank. Here we focus on the tensors of rank over , which has as a dense subset the orbit
of a single tensor under a natural group action. We construct polynomial
invariants under this group action whose non-vanishing distinguishes this orbit
from points only in its closure. Together with an explicit subset of the
defining polynomials of the variety, this gives a semialgebraic description of
the tensors of rank and multilinear rank . The polynomials we
construct coincide with Cayley's hyperdeterminant in the case , and thus
generalize it. Though our construction is direct and explicit, we also recast
our functions in the language of representation theory for additional insights.
We give three applications in different directions: First, we develop basic
topological understanding of how the real tensors of complex rank and
multilinear rank form a collection of path-connected subsets, one of
which contains tensors of real rank . Second, we use the invariants to
develop a semialgebraic description of the set of probability distributions
that can arise from a simple stochastic model with a hidden variable, a model
that is important in phylogenetics and other fields. Third, we construct simple
examples of tensors of rank which lie in the closure of those of rank
.Comment: 31 pages, 1 figur
FeH Absorption in the Near-Infrared Spectra of Late M and L Dwarfs
We present medium-resolution z-, J-, and H-band spectra of four late-type
dwarfs with spectral types ranging from M8 to L7.5. In an attempt to determine
the origin of numerous weak absorption features throughout their near-infrared
spectra, and motivated by the recent tentative identification of the E 4\Pi- A
^4\Pi system of FeH near 1.6 microns in umbral and cool star spectra, we have
compared the dwarf spectra to a laboratory FeH emission spectrum. We have
identified nearly 100 FeH absorption features in the z-, J-, and H-band spectra
of the dwarfs. In particular, we have identified 34 features which dominate the
appearance of the H-band spectra of the dwarfs and which appear in the
laboratory FeH spectrum. Finally, all of the features are either weaker or
absent in the spectrum of the L7.5 dwarf which is consistent with the weakening
of the known FeH bandheads in the spectra of the latest L dwarfs.Comment: accepted by Ap
unfixed and fixed human chromosomes show different staining patterns after restriction endonuclease digestion
Restriction endonucleases (REs) have been widely used to produce banding patterns on chromosomes, but it remains uncertain to what extent the patterns are due to the sequence specificity of the enzymes, and to what extent chromatin structure influences the pattern of digestion. To throw light on this question, we have digested with restriction endonucleases unfixed chromosomes prepared in two different ways (isolated, and whole metaphase cells spread with a cytocentrifuge) and compared the results with those obtained on conventionally fixed chromosomes. Unfixed isolated chromosomes are easily destroyed by REs; after fixation with cold methanol, which produced minimal alteration to the chromatin structure, the chromosomes are resistant to the action of REs, and conventional methanol-acetic acid fixation is required to permit the induction of banding patterns by REs. Unfixed cytocentrifuge preparations, in which the chromosomes are still surrounded by cytoplasm, are much more resistant to the action of REs, and again banding patterns were only induced after methanol-acetic acid fixation. We conclude that the action of restriction endonucleases on chromosomes is strongly influenced by chromatin organisation, and that methanol-acetic acid fixation is required to permit the induction of conventional banding patterns on chromosomes
Experimental Investigation of Optimized Cold-formed Steel Compression Members
In the past, standard C - shaped metal studs have been the only option for designers and contractors when selecting a cross section for load bearing compression members. T he sigma shaped section has recently emerged as an alternative to the C - section. The sigma shaped section is very similar to the C - shape, with the exception of having an intermediate web return and complex stiffeners. The experimental results of concentric axial compression tests of fifty - eight sigma shaped members are reported. Specimen s were tested at various lengths to force global, distortional, and local buckling failure modes. Additionally, the test program contained members with and without web holes. Comparisons of experimental results with the American Iron and Steel Institute ( AISI) design methods, Effective Width Method (EWM) and Direct Strength Method (DSM), are discussed
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Energetic and Environmental Constraints on the Community Structure of Benthic Microbial Mats in Lake Fryxell, Antarctica.
Ecological communities are regulated by the flow of energy through environments. Energy flow is typically limited by access to photosynthetically active radiation (PAR) and oxygen concentration (O2). The microbial mats growing on the bottom of Lake Fryxell, Antarctica, have well-defined environmental gradients in PAR and (O2). We analyzed the metagenomes of layers from these microbial mats to test the extent to which access to oxygen and light controls community structure. We found variation in the diversity and relative abundances of Archaea, Bacteria and Eukaryotes across three (O2) and PAR conditions: high (O2) and maximum PAR, variable (O2) with lower maximum PAR, and low (O2) and maximum PAR. We found distinct communities structured by the optimization of energy use on a millimeter-scale across these conditions. In mat layers where (O2) was saturated, PAR structured the community. In contrast, (O2) positively correlated with diversity and affected the distribution of dominant populations across the three habitats, suggesting that meter-scale diversity is structured by energy availability. Microbial communities changed across covarying gradients of PAR and (O2). The comprehensive metagenomic analysis suggests that the benthic microbial communities in Lake Fryxell are structured by energy flow across both meter- and millimeter-scales
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