361 research outputs found
Near infrared spectroscopy of the type IIn SN 2010jl: evidence for high velocity ejecta
The Type IIn supernova SN 2010jl was relatively nearby and luminous, allowing
detailed studies of the near-infrared (NIR) emission. We present 1 - 2.4 micron
spectroscopy over the age range of 36 - 565 days from the earliest detection of
the supernova. On day 36, the H lines show an unresolved narrow emission
component along with a symmetric broad component that can be modeled as the
result of electron scattering by a thermal distribution of electrons. Over the
next hundreds of days, the broad components of the H lines shift to the blue by
700 km/s, as is also observed in optical lines. The narrow lines do not show a
shift, indicating they originate in a different region. He I 1.0830 and 2.0587
micron lines both show an asymmetric broad emission component, with a shoulder
on the blue side that varies in prominence and velocity from -5500 km/s on day
108 to -4000 km/s on day 219. This component may be associated with the higher
velocity flow indicated by X-ray observations of the supernova. The absence of
the feature in the H lines suggests that this is from a He rich ejecta flow.
The He I 1.0830 micron feature has a narrow P Cygni line, with absorption
extending to ~100 km/s and strengthening over the first 200 days, and an
emission component which weakens with time. At day 403, the continuum emission
becomes dominated by a blackbody spectrum with a temperature of ~1900 K,
suggestive of dust emission.Comment: 17 pages, 18 figure
Online Detection of Repetitions with Backtracking
In this paper we present two algorithms for the following problem: given a
string and a rational , detect in the online fashion the earliest
occurrence of a repetition of exponent in the string.
1. The first algorithm supports the backtrack operation removing the last
letter of the input string. This solution runs in time and
space, where is the maximal length of a string generated during the
execution of a given sequence of read and backtrack operations.
2. The second algorithm works in time and space,
where is the length of the input string and is the number of
distinct letters. This algorithm is relatively simple and requires much less
memory than the previously known solution with the same working time and space.
a string generated during the execution of a given sequence of read and
backtrack operations.Comment: 12 pages, 5 figures, accepted to CPM 201
Pattern Matching in Multiple Streams
We investigate the problem of deterministic pattern matching in multiple
streams. In this model, one symbol arrives at a time and is associated with one
of s streaming texts. The task at each time step is to report if there is a new
match between a fixed pattern of length m and a newly updated stream. As is
usual in the streaming context, the goal is to use as little space as possible
while still reporting matches quickly. We give almost matching upper and lower
space bounds for three distinct pattern matching problems. For exact matching
we show that the problem can be solved in constant time per arriving symbol and
O(m+s) words of space. For the k-mismatch and k-difference problems we give
O(k) time solutions that require O(m+ks) words of space. In all three cases we
also give space lower bounds which show our methods are optimal up to a single
logarithmic factor. Finally we set out a number of open problems related to
this new model for pattern matching.Comment: 13 pages, 1 figur
A suffix tree or not a suffix tree?
In this paper we study the structure of suffix trees. Given an unlabeled tree τ on n nodes and suffix links of its internal nodes, we ask the question ”Is τ a suffix tree?”, i.e., is there a string S whose suffix tree has the same topological structure as τ? We place no restrictions on S, in particular we do not require that S ends with a unique symbol. This corresponds to considering the more general definition of implicit or extended suffix trees. Such general suffix trees have many applications and are for example needed to allow efficient updates when suffix trees are built online. Deciding if τ is a suffix tree is not an easy task, because, with no restrictions on the final symbol, we cannot guess the length of a string that realizes τ from the number of leaves. And without an upper bound on the length of such a string, it is not even clear how to solve the problem by an exhaustive search. In this paper, we prove that τ is a suffix tree if and only if it is realized by a string S of length n−1, and we give a linear-time algorithm for inferring S when the first letter on each edge is known. This generalizes the work of I et al. [Discrete Appl. Math. 163, 2014]
Unzipping Kinetics of Double-Stranded DNA in a Nanopore
We studied the unzipping kinetics of single molecules of double-stranded DNA
by pulling one of their two strands through a narrow protein pore. PCR analysis
yielded the first direct proof of DNA unzipping in such a system. The time to
unzip each molecule was inferred from the ionic current signature of DNA
traversal. The distribution of times to unzip under various experimental
conditions fit a simple kinetic model. Using this model, we estimated the
enthalpy barriers to unzipping and the effective charge of a nucleotide in the
pore, which was considerably smaller than previously assumed.Comment: 10 pages, 5 figures, Accepted: Physics Review Letter
Application of COMPOCHIP Microarray to Investigate the Bacterial Communities of Different Composts
A microarray spotted with 369 different 16S rRNA gene probes specific to microorganisms involved in the degradation process of organic waste during composting was developed. The microarray was tested with pure cultures, and of the 30,258 individual probe-target hybridization reactions performed, there were only 188 false positive (0.62%) and 22 false negative signals (0.07%). Labeled target DNA was prepared by polymerase chain reaction amplification of 16S rRNA genes using a Cy5-labeled universal bacterial forward primer and a universal reverse primer. The COMPOCHIP microarray was applied to three different compost types (green compost, manure mix compost, and anaerobic digestate compost) of different maturity (2, 8, and 16 weeks), and differences in the microorganisms in the three compost types and maturity stages were observed. Multivariate analysis showed that the bacterial composition of the three composts was different at the beginning of the composting process and became more similar upon maturation. Certain probes (targeting Sphingobacterium, Actinomyces, Xylella/Xanthomonas/ Stenotrophomonas, Microbacterium, Verrucomicrobia, Planctomycetes, Low G + C and Alphaproteobacteria) were more influential in discriminating between different composts. Results from denaturing gradient gel electrophoresis supported those of microarray analysis. This study showed that the COMPOCHIP array is a suitable tool to study bacterial communities in composts
Single Molecule Statistics and the Polynucleotide Unzipping Transition
We present an extensive theoretical investigation of the mechanical unzipping
of double-stranded DNA under the influence of an applied force. In the limit of
long polymers, there is a thermodynamic unzipping transition at a critical
force value of order 10 pN, with different critical behavior for homopolymers
and for random heteropolymers. We extend results on the disorder-averaged
behavior of DNA's with random sequences to the more experimentally accessible
problem of unzipping a single DNA molecule. As the applied force approaches the
critical value, the double-stranded DNA unravels in a series of discrete,
sequence-dependent steps that allow it to reach successively deeper energy
minima. Plots of extension versus force thus take the striking form of a series
of plateaus separated by sharp jumps. Similar qualitative features should
reappear in micromanipulation experiments on proteins and on folded RNA
molecules. Despite their unusual form, the extension versus force curves for
single molecules still reveal remnants of the disorder-averaged critical
behavior. Above the transition, the dynamics of the unzipping fork is related
to that of a particle diffusing in a random force field; anomalous,
disorder-dominated behavior is expected until the applied force exceeds the
critical value for unzipping by roughly 5 pN.Comment: 40 pages, 18 figure
Longest Common Extensions in Trees
The longest common extension (LCE) of two indices in a string is the length
of the longest identical substrings starting at these two indices. The LCE
problem asks to preprocess a string into a compact data structure that supports
fast LCE queries. In this paper we generalize the LCE problem to trees and
suggest a few applications of LCE in trees to tries and XML databases. Given a
labeled and rooted tree of size , the goal is to preprocess into a
compact data structure that support the following LCE queries between subpaths
and subtrees in . Let , , , and be nodes of such
that and are descendants of and respectively.
\begin{itemize} \item \LCEPP(v_1, w_1, v_2, w_2): (path-path \LCE) return
the longest common prefix of the paths and . \item \LCEPT(v_1, w_1, v_2): (path-tree \LCE) return maximal
path-path LCE of the path and any path from to a
descendant leaf. \item \LCETT(v_1, v_2): (tree-tree \LCE) return a maximal
path-path LCE of any pair of paths from and to descendant leaves.
\end{itemize} We present the first non-trivial bounds for supporting these
queries. For \LCEPP queries, we present a linear-space solution with
query time. For \LCEPT queries, we present a linear-space
solution with query time, and complement this with a
lower bound showing that any path-tree LCE structure of size O(n \polylog(n))
must necessarily use time to answer queries. For \LCETT
queries, we present a time-space trade-off, that given any parameter , , leads to an space and query-time
solution. This is complemented with a reduction to the the set intersection
problem implying that a fast linear space solution is not likely to exist
- …