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 $n$ 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 $O(\log^2 n)$ amortized time per edge insertion or deletion, and $O(\log n / \log\log n)$ 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 $\Delta$ is the average batch size of all deletions, our algorithm achieves $O(\log n \log(1 + n / \Delta))$ expected amortized work per edge insertion and deletion and $O(\log^3 n)$ depth w.h.p. Our algorithm answers a batch of $k$ connectivity queries in $O(k \log(1 + n/k))$ expected work and $O(\log n)$ 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