17,153 research outputs found
Comment on "Can one predict DNA Transcription Start Sites by Studying Bubbles?"
Comment on T.S. van Erp, S. Cuesta-Lopez, J.-G. Hagmann, and M. Peyrard,
Phys. Rev. Lett. 95, 218104 (2005) [arXiv: physics/0508094]
Healing Length and Bubble Formation in DNA
We have recently suggested that the probability for the formation of
thermally activated DNA bubbles is, to a very good approximation, proportional
to the number of soft AT pairs over a length L(n) that depend on the size
of the bubble and on the temperature of the DNA. Here we clarify the physical
interpretation of this length by relating it to the (healing) length that is
required for the effect of a base-pair defect to become neligible. This
provides a simple criteria to calculate L(n) for bubbles of arbitrary size and
for any temperature of the DNA. We verify our findings by exact calculations of
the equilibrium statistical properties of the Peyrard-Bishop-Dauxois model. Our
method permits calculations of equilibrium thermal openings with several order
of magnitude less numerical expense as compared with direct evaluations
Theory of Bubble Nucleation and Cooperativity in DNA Melting
The onset of intermediate states (denaturation bubbles) and their role during
the melting transition of DNA are studied using the Peyrard-Bishop-Daxuois
model by Monte Carlo simulations with no adjustable parameters. Comparison is
made with previously published experimental results finding excellent
agreement. Melting curves, critical DNA segment length for stability of bubbles
and the possibility of a two states transition are studied.Comment: 4 figures. Accepted for publication in Physical Review Letter
X-Ray Emission from the Warm Hot Intergalactic Medium
The number of detected baryons in the Universe at z<0.5 is much smaller than
predicted by standard big bang nucleosynthesis and by the detailed observation
of the Lyman alpha forest at red-shift z=2. Hydrodynamical simulations indicate
that a large fraction of the baryons today is expected to be in a ``warm-hot''
(10^5-10^7K) filamentary gas, distributed in the intergalactic medium. This
gas, if it exists, should be observable only in the soft X-ray and UV bands.
Using the predictions of a particular hydrodynamic model, we simulated the
expected X-ray flux as a function of energy in the 0.1-2 keV band due to the
Warm-Hot Intergalactic Medium (WHIM), and compared it with the flux from local
and high red-shift diffuse components. Our results show that as much as 20% of
the total diffuse X-ray background (DXB) in the energy range 0.37-0.925keV
could be due to X-ray flux from the WHIM, 70% of which comes from filaments at
redshift z between 0.1 and 0.6. Simulations done using a FOV of 3', comparable
with that of Suzaku and Constellation-X, show that in more than 20% of the
observations we expect the WHIM flux to contribute to more than 20% of the DXB.
These simulations also show that in about 10% of all the observations a single
bright filament in the FOV accounts, alone, for more than 20% of the DXB flux.
Red-shifted oxygen lines should be clearly visible in these observations.Comment: 19 pages, 6 figure
Parallel Batch-Dynamic Graph Connectivity
In this paper, we study batch parallel algorithms for the dynamic
connectivity problem, a fundamental problem that has received considerable
attention in the sequential setting. The most well known sequential algorithm
for dynamic connectivity is the elegant level-set algorithm of Holm, de
Lichtenberg and Thorup (HDT), which achieves amortized time per
edge insertion or deletion, and time per query. We
design a parallel batch-dynamic connectivity algorithm that is work-efficient
with respect to the HDT algorithm for small batch sizes, and is asymptotically
faster when the average batch size is sufficiently large. Given a sequence of
batched updates, where is the average batch size of all deletions, our
algorithm achieves expected amortized work per
edge insertion and deletion and depth w.h.p. Our algorithm
answers a batch of connectivity queries in expected
work and depth w.h.p. To the best of our knowledge, our algorithm
is the first parallel batch-dynamic algorithm for connectivity.Comment: This is the full version of the paper appearing in the ACM Symposium
on Parallelism in Algorithms and Architectures (SPAA), 201
Gaussian Approximation Potentials: the accuracy of quantum mechanics, without the electrons
We introduce a class of interatomic potential models that can be
automatically generated from data consisting of the energies and forces
experienced by atoms, derived from quantum mechanical calculations. The
resulting model does not have a fixed functional form and hence is capable of
modeling complex potential energy landscapes. It is systematically improvable
with more data. We apply the method to bulk carbon, silicon and germanium and
test it by calculating properties of the crystals at high temperatures. Using
the interatomic potential to generate the long molecular dynamics trajectories
required for such calculations saves orders of magnitude in computational cost.Comment: v3-4: added new material and reference
Lengthscales and Cooperativity in DNA Bubble Formation
It appears that thermally activated DNA bubbles of different sizes play
central roles in important genetic processes. Here we show that the probability
for the formation of such bubbles is regulated by the number of soft AT pairs
in specific regions with lengths which at physiological temperatures are of the
order of (but not equal to) the size of the bubble. The analysis is based on
the Peyrard- Bishop-Dauxois model, whose equilibrium statistical properties
have been accurately calculated here with a transfer integral approach
Research study of some RAM antennas Final report, 18 Nov. 1964 - 18 Jun. 1965
Input impedance and radiation pattern determinations for cylindrical gap, waveguide excited and circular waveguide slot antenna array
A note on Kerr/CFT and free fields
The near-horizon geometry of the extremal four-dimensional Kerr black hole
and certain generalizations thereof has an SL(2,R) x U(1) isometry group.
Excitations around this geometry can be controlled by imposing appropriate
boundary conditions. For certain boundary conditions, the U(1) isometry is
enhanced to a Virasoro algebra. Here, we propose a free-field construction of
this Virasoro algebra.Comment: 10 pages, v2: comments and references adde
Hanle effect in coherent backscattering
We study the shape of the coherent backscattering (CBS) cone obtained when
resonant light illuminates a thick cloud of laser-cooled rubidium atoms in
presence of a homogenous magnetic field. We observe new magnetic
field-dependent anisotropies in the CBS signal. We show that the observed
behavior is due to the modification of the atomic radiation pattern by the
magnetic field (Hanle effect in the excited state).Comment: 4 pages, 3 figure
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