1,601 research outputs found
Q-stars and charged q-stars
We present the formalism of q-stars with local or global U(1) symmetry. The
equations we formulate are solved numerically and provide the main features of
the soliton star. We study its behavior when the symmetry is local in contrast
to the global case. A general result is that the soliton remains stable and
does not decay into free particles and the electrostatic repulsion preserves it
from gravitational collapse. We also investigate the case of a q-star with
non-minimal energy-momentum tensor and find that the soliton is stable even in
some cases of collapse when the coupling to gravity is absent.Comment: Latex, 19pg, 12 figures. Accepted in Phys. Rev.
Biases in the Experimental Annotations of Protein Function and their Effect on Our Understanding of Protein Function Space
The ongoing functional annotation of proteins relies upon the work of
curators to capture experimental findings from scientific literature and apply
them to protein sequence and structure data. However, with the increasing use
of high-throughput experimental assays, a small number of experimental studies
dominate the functional protein annotations collected in databases. Here we
investigate just how prevalent is the "few articles -- many proteins"
phenomenon. We examine the experimentally validated annotation of proteins
provided by several groups in the GO Consortium, and show that the distribution
of proteins per published study is exponential, with 0.14% of articles
providing the source of annotations for 25% of the proteins in the UniProt-GOA
compilation. Since each of the dominant articles describes the use of an assay
that can find only one function or a small group of functions, this leads to
substantial biases in what we know about the function of many proteins.
Mass-spectrometry, microscopy and RNAi experiments dominate high throughput
experiments. Consequently, the functional information derived from these
experiments is mostly of the subcellular location of proteins, and of the
participation of proteins in embryonic developmental pathways. For some
organisms, the information provided by different studies overlap by a large
amount. We also show that the information provided by high throughput
experiments is less specific than those provided by low throughput experiments.
Given the experimental techniques available, certain biases in protein function
annotation due to high-throughput experiments are unavoidable. Knowing that
these biases exist and understanding their characteristics and extent is
important for database curators, developers of function annotation programs,
and anyone who uses protein function annotation data to plan experiments.Comment: Accepted to PLoS Computational Biology. Press embargo applies. v4:
text corrected for style and supplementary material inserte
Spectral Boundary of Positive Random Potential in a Strong Magnetic Field
We consider the problem of randomly distributed positive delta-function
scatterers in a strong magnetic field and study the behavior of density of
states close to the spectral boundary at in both two and
three dimensions. Starting from dimensionally reduced expression of Brezin et
al. and using the semiclassical approximation we show that the density of
states in the Lifshitz tail at small energies is proportio- nal to in
two dimensions and to in three
dimensions, where is the energy and is the density of scatterers in
natural units.Comment: 12 pages, LaTex, 5 figures available upon request, to appear in Phys.
Rev.
The Importance of DNA Repair in Tumor Suppression
The transition from a normal to cancerous cell requires a number of highly
specific mutations that affect cell cycle regulation, apoptosis,
differentiation, and many other cell functions. One hallmark of cancerous
genomes is genomic instability, with mutation rates far greater than those of
normal cells. In microsatellite instability (MIN tumors), these are often
caused by damage to mismatch repair genes, allowing further mutation of the
genome and tumor progression. These mutation rates may lie near the error
catastrophe found in the quasispecies model of adaptive RNA genomes, suggesting
that further increasing mutation rates will destroy cancerous genomes. However,
recent results have demonstrated that DNA genomes exhibit an error threshold at
mutation rates far lower than their conservative counterparts. Furthermore,
while the maximum viable mutation rate in conservative systems increases
indefinitely with increasing master sequence fitness, the semiconservative
threshold plateaus at a relatively low value. This implies a paradox, wherein
inaccessible mutation rates are found in viable tumor cells. In this paper, we
address this paradox, demonstrating an isomorphism between the conservatively
replicating (RNA) quasispecies model and the semiconservative (DNA) model with
post-methylation DNA repair mechanisms impaired. Thus, as DNA repair becomes
inactivated, the maximum viable mutation rate increases smoothly to that of a
conservatively replicating system on a transformed landscape, with an upper
bound that is dependent on replication rates. We postulate that inactivation of
post-methylation repair mechanisms are fundamental to the progression of a
tumor cell and hence these mechanisms act as a method for prevention and
destruction of cancerous genomes.Comment: 7 pages, 5 figures; Approximation replaced with exact calculation;
Minor error corrected; Minor changes to model syste
In-medium Yang-Mills equations: a derivation and canonical quantization
The equations for Yang-Mills field in a medium are derived in a linear
approximation with respect to the gauge coupling parameter and the external
field. The obtained equations closely resemble the macroscopic Maxwell
equations. A canonical quantization is performed for a family of Fermi-like
gauges in the case of constant and diagonal (in the group indices) tensors of
electric permittivity and magnetic permeability. The physical subspace is
defined and the gauge field propagator is evaluated for a particular choice of
the gauge. The propagator is applied for evaluation of the cross-section of
ellastic quark scattering in the Born approximation. Possible applications to
Cherenkov-type gluon radiation are commented briefly.Comment: 27 pages, references added, version extended with emphasis on
non-Abelian gauge group impact on medium characteristics. To appear in J.
Phys.
Superradiance from an ultrathin film of three-level V-type atoms: Interplay between splitting, quantum coherence and local-field effects
We carry out a theoretical study of the collective spontaneous emission
(superradiance) from an ultrathin film comprised of three-level atoms with
-configuration of the operating transitions. As the thickness of the system
is small compared to the emission wavelength inside the film, the local-field
correction to the averaged Maxwell field is relevant. We show that the
interplay between the low-frequency quantum coherence within the subspace of
the upper doublet states and the local-field correction may drastically affect
the branching ratio of the operating transitions. This effect may be used for
controlling the emission process by varying the doublet splitting and the
amount of low-frequency coherence.Comment: 15 pages, 5 figure
Bogomol'nyi Equations of Maxwell-Chern-Simons vortices from a generalized Abelian Higgs Model
We consider a generalization of the abelian Higgs model with a Chern-Simons
term by modifying two terms of the usual Lagrangian. We multiply a dielectric
function with the Maxwell kinetic energy term and incorporate nonminimal
interaction by considering generalized covariant derivative. We show that for a
particular choice of the dielectric function this model admits both topological
as well as nontopological charged vortices satisfying Bogomol'nyi bound for
which the magnetic flux, charge and angular momentum are not quantized. However
the energy for the topolgical vortices is quantized and in each sector these
topological vortex solutions are infinitely degenerate. In the nonrelativistic
limit, this model admits static self-dual soliton solutions with nonzero finite
energy configuration. For the whole class of dielectric function for which the
nontopological vortices exists in the relativistic theory, the charge density
satisfies the same Liouville equation in the nonrelativistic limit.Comment: 30 pages(4 figures not included), RevTeX, IP/BBSR/93-6
Oscillons: Resonant Configurations During Bubble Collapse
Oscillons are localized, non-singular, time-dependent, spherically-symmetric
solutions of nonlinear scalar field theories which, although unstable, are
extremely long-lived. We show that they naturally appear during the collapse of
subcritical bubbles in models with symmetric and asymmetric double-well
potentials. By a combination of analytical and numerical work we explain
several of their properties, including the conditions for their existence,
their longevity, and their final demise. We discuss several contexts in which
we expect oscillons to be relevant. In particular, their nucleation during
cosmological phase transitions may have wide-ranging consequences.Comment: 31 pages Revtex, 20 uufiles-encoded figures. Section "Possible
Applications of Oscillons" slightly expande
Cooperative Spontaneous Emission as a Many Body Eigenvalue Problem
We study emission of a single photon from a spherically symmetric cloud of N
atoms (one atom is excited, N-1 are in ground state) and present an exact
analytical expression for eigenvalues and eigenstates of this many body
problem. We found that some states decay much faster then the single-atom decay
rate, while other states are trapped and undergo very slow decay. When size of
the atomic cloud is small compared with the radiation wave length we found that
the radiation frequency undergoes a large shift.Comment: 5 pages, 3 figures, to appear in Physical Review
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