256 research outputs found
Identifying short motifs by means of extreme value analysis
The problem of detecting a binding site -- a substring of DNA where
transcription factors attach -- on a long DNA sequence requires the recognition
of a small pattern in a large background. For short binding sites, the matching
probability can display large fluctuations from one putative binding site to
another. Here we use a self-consistent statistical procedure that accounts
correctly for the large deviations of the matching probability to predict the
location of short binding sites. We apply it in two distinct situations: (a)
the detection of the binding sites for three specific transcription factors on
a set of 134 estrogen-regulated genes; (b) the identification, in a set of 138
possible transcription factors, of the ones binding a specific set of nine
genes. In both instances, experimental findings are reproduced (when available)
and the number of false positives is significantly reduced with respect to the
other methods commonly employed.Comment: 6 pages, 5 figure
Distribution of hammerhead and hammerhead-like RNA motifs through the GenBank
Hammerhead ribozymes previously were found in satellite RNAs from plant viroids and in repetitive DNA from certain species of newts and schistosomes. To determine if this catalytic RNA motif has a wider distribution, we decided to scrutinize the GenBank database for RNAs that contain hammerhead or hammerhead-like motifs. The search shows a widespread distribution of this kind of RNA motif in different sequences suggesting that they might have a more general role in RNA biology. The frequency of the hammerhead motif is half of that expected from a random distribution, but this fact comes From the low CpG representation in vertebrate sequences and the bias of the GenBank for those sequences. Intriguing motifs include those found in several families of repetitive sequences, in the satellite RNA from the carrot red leaf luteovirus, in plant viruses like the spinach latent virus and the elm mottle virus, in animal viruses like the hepatitis E virus and the caprine encephalitis virus, and in mRNAs such as those coding for cytochrome P450 oxidoreductase in the rat and the hamster
Aspects of classical and quantum motion on a flux cone
Motion of a non-relativistic particle on a cone with a magnetic flux running
through the cone axis (a ``flux cone'') is studied. It is expressed as the
motion of a particle moving on the Euclidean plane under the action of a
velocity-dependent force. Probability fluid (``quantum flow'') associated with
a particular stationary state is studied close to the singularity,
demonstrating non trivial Aharonov-Bohm effects. For example, it is shown that
near the singularity quantum flow departs from classical flow. In the context
of the hydrodynamical approach to quantum mechanics, quantum potential due to
the conical singularity is determined and the way it affects quantum flow is
analysed. It is shown that the winding number of classical orbits plays a role
in the description of the quantum flow. Connectivity of the configuration space
is also discussed.Comment: LaTeX file, 21 pages, 8 figure
Approach to Perturbative Results in the N-Delta Transition
We show that constraints from perturbative QCD calculations play a role in
the nucleon to Delta(1232) electromagnetic transition even at moderate momentum
transfer scales. The pQCD constraints, tied to real photoproduction data and
unseparated resonance response functions, lead to explicit forms for the
helicity amplitudes wherein the E2/M1 ratio remains small at moderately large
momentum transfer.Comment: 4 pages, 2 figures, ReVTe
Hamiltonian structure of 2+1 dimensional gravity
A summary is given of some results and perspectives of the hamiltonian ADM
approach to 2+1 dimensional gravity. After recalling the classical results for
closed universes in absence of matter we go over the the case in which matter
is present in the form of point spinless particles. Here the maximally slicing
gauge proves most effective by relating 2+1 dimensional gravity to the Riemann-
Hilbert problem. It is possible to solve the gravitational field in terms of
the particle degrees of freedom thus reaching a reduced dynamics which involves
only the particle positions and momenta. Such a dynamics is proven to be
hamiltonian and the hamiltonian is given by the boundary term in the
gravitational action. As an illustration the two body hamiltonian is used to
provide the canonical quantization of the two particle system.Comment: 13 pages,2 figures,latex, Plenary talk at SIGRAV2000 Conferenc
Perturbative Renormalizations of Anyon Quantum Mechanics
In bosonic end perturbative calculations for quantum mechanical anyon systems
a regularization and renormalization procedure, analogous to those used in
field theory, is necessary. I examine the reliability and the physical
interpretation of the most commonly used bosonic end regularization procedures.
I then use the regularization procedure with the most transparent physical
interpretation to derive some bosonic end perturbation theory results on anyon
spectra, including a 3-anyon ground state energy.Comment: 19 pages, Plain LaTex, MIT-CTP-232
Nucleon to Delta Weak Excitation Amplitudes in the Non-relativistic Quark Model
We investigate the nucleon to Delta(1232) vector and axial vector amplitudes
in the non-relativistic quark model of the Isgur-Karl variety. A particular
interest is to investigate the SU(6) symmetry breaking, due to color hyperfine
interaction. We compare the theoretical estimates to recent experimental
investigation of the Adler amplitudes by neutrino scattering.Comment: \documentstyle[aps]{revtex}, 21pages; 11 postscript figures. Accepted
for publication by Phys. Rev.
Effective Lagrangian Approach to the Theory of Eta Photoproduction in the Region
We investigate eta photoproduction in the resonance region
within the effective Lagrangian approach (ELA), wherein leading contributions
to the amplitude at the tree level are taken into account. These include the
nucleon Born terms and the leading -channel vector meson exchanges as the
non-resonant pieces. In addition, we consider five resonance contributions in
the - and - channel; besides the dominant , these are:
and . The amplitudes for the
and the photoproduction near threshold have significant
differences, even as they share common contributions, such as those of the
nucleon Born terms. Among these differences, the contribution to the
photoproduction of the -channel excitation of the is the most
significant. We find the off-shell properties of the spin-3/2 resonances to be
important in determining the background contributions. Fitting our effective
amplitude to the available data base allows us to extract the quantity
, characteristic of the
photoexcitation of the resonance and its decay into the
-nucleon channel, of interest to precise tests of hadron models. At the
photon point, we determine it to be from
the old data base, and from a
combination of old data base and new Bates data. We obtain the helicity
amplitude for to be from the old data base, and from the combination of the old data base and new Bates
data, compared with the results of the analysis of pion photoproduction
yielding , in the same units.Comment: 43 pages, RevTeX, 9 figures available upon request, to appear in
Phys. Rev.
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