Efficient chaining of seeds in ordered trees

We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem is a natural extension of a similar problem for sequences, and has applications in computational biology, such as mining a database of RNA secondary structures. For the chaining problem with a set of m constant size seeds, we describe an algorithm with complexity O(m2 log(m)) in time and O(m2) in space

Decay Modes of Unstable Strings in Plane-Wave String Field Theory

The cubic interaction vertex of light-cone string field theory in the plane-wave background has a simple effective form when considering states with only bosonic excitations. This simple effective interaction vertex is used in this paper to calculate the three string interaction matrix elements for states of arbitrary bosonic excitation and these results are used to examine certain decay modes on the mass-shell. It is shown that the matrix elements of one string to two string decays involving only bosonic excitations will vanish to all orders in 1/mu on the mass-shell when the number of excitations on the initial string is less than or equal to two, but in general will not vanish when the number of excitations is greater than two. Also, a truncated calculation of the mass-shell matrix elements for one string to three string decays of two excitation states is performed and suggests that these matrix elements do not vanish on the mass-shell. There is, however, a quantitative discrepancy between this last result and its (also non-vanishing) gauge theory prediction from the BMN correspondence.Comment: 11 pages; v2: references added; v3: normalization of interaction vertex and corresponding amplitudes changed by a factor of mu to reflect SFT normalization (must now divide by mu to compare with BMN dual gauge theory), and minor errors correcte

Temperatures of Fragment Kinetic Energy Spectra

Multifragmentation reactions without large compression in the initial state (proton-induced reactions, reverse-kinematics, projectile fragmentation) are examined, and it is verified quantitatively that the high temperatures obtained from fragment kinetic energy spectra and lower temperatures obtained from observables such as level population or isotope ratios can be understood in a common framework.Comment: LaTeX, 7 pages, 2 figures available from autho

Comments on Supersymmetry Algebra and Contact Term in Matrix String Theory

Following hep-th/0309238 relating the matrix string theory to the light-cone superstring field theory, we write down two supercharges in the matrix string theory explicitly. After checking the supersymmetry algebra at the leading order, we proceed to discuss higher-order contact terms.Comment: 17 pages, no figures, v2: eq. (5.1) and related appendices corrected, v3: final version to appear in JHE

Predictions for PP-wave string amplitudes from perturbative SYM

The role of general two-impurity multi-trace operators in the BMN correspondence is explored. Surprisingly, the anomalous dimensions of all two-impurity multi-trace BMN operators to order g_2^2\lambda' are completely determined in terms of single-trace anomalous dimensions. This is due to suppression of connected field theory diagrams in the BMN limit and this fact has important implications for some string theory processes on the PP-wave background. We also make gauge theory predictions for the matrix elements of the light-cone string field theory Hamiltonian in the two string-two string and one string-three string sectors.Comment: 46 pages, 12 figures. V3:typos correcte

On light-cone SFT contact terms in a plane wave

Testing the BMN correspondence at non-zero string coupling g_s requires a one-loop string field theory calculation. At order g_s^2, matrix elements of the light-cone string field theory Hamiltonian between single-string states receive two contributions: the iterated cubic interaction, and a contact term {Q, Q} whose presence is dictated by supersymmetry. In this paper we calculate the leading large mu p^+ alpha' contribution from both terms for the set of intermediate states with two string excitations. We find precise agreement with the basis-independent order g_2^2 results from gauge theory.Comment: 15 pages, 1 figur

Instability and Degeneracy in the BMN Correspondence

Non-degenerate perturbation theory, which was used to calculate the scale dimension of operators on the gauge theory side of the correspondence, breaks down when effects of triple trace operators are included. We interpret this as an instability of excited single-string states in the dual string theory for decay into the continuum of degenerate 3-string states. We apply time-dependent perturbation theory to calculate the decay widths from gauge theory. These widths are new gauge theory data which can be compared with future calculations in light cone string field theory.Comment: 23 pages, no figure

Differential effects of retinoic acid isomers on the expression of nuclear receptor co-regulators in neuroblastoma

AbstractRetinoic acid modulates growth and induces differentiation and apoptosis of neuroblastoma cells in vitro, with the all-trans and 9-cis isomers having different biological properties. Transcriptional activation in response to retinoic acid isomers is mediated by retinoic acid receptors and retinoid X receptors. The differential expression of co-activators and co-repressors which preferentially interact with retinoic acid receptors or retinoid X receptors may be a mechanism leading to different cellular responses to 9-cis and all-trans retinoic acid. To test this hypothesis, we have studied the expression of the nuclear receptor co-regulators TIF1α, TIF1β, SUG1 and SMRT in the N-type and S-type neuroblastoma cell lines SH SY 5Y and SH S EP. Transcripts for all four co-regulators were expressed in these neuroblastoma cells. The expression of TIF1α, TIF1β and SUG1 did not change in response to retinoic acid; however, SMRT was induced in both neuroblastoma cell lines, but particularly by all-trans retinoic acid in SH S EP cells. An additional co-activator, Trip3, was isolated by differential mRNA display and shown to be preferentially induced by 9-cis retinoic acid in SH SY 5Y and SH S EP cells. These data suggest that retinoic acid isomer-specific induction of nuclear receptor co-regulators may determine, in part, the differential biological effects of retinoic acid isomers

Transport of charged particles by adjusting rf voltage amplitudes

We propose a planar architecture for scalable quantum information processing (QIP) that includes X-junctions through which particles can move without micromotion. This is achieved by adjusting radio frequency (rf) amplitudes to move an rf null along the legs of the junction. We provide a proof-of-principle by transporting dust particles in three dimensions via adjustable rf potentials in a 3D trap. For the proposed planar architecture, we use regularization techniques to obtain amplitude settings that guarantee smooth transport through the X-junction.Comment: 16 pages, 10 figure