An Efficient Algorithm For Chinese Postman Walk on Bi-directed de Bruijn Graphs

Sequence assembly from short reads is an important problem in biology. It is known that solving the sequence assembly problem exactly on a bi-directed de Bruijn graph or a string graph is intractable. However finding a Shortest Double stranded DNA string (SDDNA) containing all the k-long words in the reads seems to be a good heuristic to get close to the original genome. This problem is equivalent to finding a cyclic Chinese Postman (CP) walk on the underlying un-weighted bi-directed de Bruijn graph built from the reads. The Chinese Postman walk Problem (CPP) is solved by reducing it to a general bi-directed flow on this graph which runs in O(|E|2 log2(|V |)) time. In this paper we show that the cyclic CPP on bi-directed graphs can be solved without reducing it to bi-directed flow. We present a ?(p(|V | + |E|) log(|V |) + (dmaxp)3) time algorithm to solve the cyclic CPP on a weighted bi-directed de Bruijn graph, where p = max{|{v|din(v) - dout(v) > 0}|, |{v|din(v) - dout(v) < 0}|} and dmax = max{|din(v) - dout(v)}. Our algorithm performs asymptotically better than the bidirected flow algorithm when the number of imbalanced nodes p is much less than the nodes in the bi-directed graph. From our experimental results on various datasets, we have noticed that the value of p/|V | lies between 0.08% and 0.13% with 95% probability

Cerulean: A hybrid assembly using high throughput short and long reads

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking regions. The emergence of third generation sequencing (Pacific Biosciences) with long reads enables the opportunity to resolve complicated repeats that could not be resolved by the short read data. However, these long reads have high error rate and it is an uphill task to assemble the genome without using additional high quality short reads. Recently, Koren et al. 2012 proposed an approach to use high quality short reads data to correct these long reads and, thus, make the assembly from long reads possible. However, due to the large size of both dataset (short and long reads), error-correction of these long reads requires excessively high computational resources, even on small bacterial genomes. In this work, instead of error correction of long reads, we first assemble the short reads and later map these long reads on the assembly graph to resolve repeats. Contribution: We present a hybrid assembly approach that is both computationally effective and produces high quality assemblies. Our algorithm first operates with a simplified version of the assembly graph consisting only of long contigs and gradually improves the assembly by adding smaller contigs in each iteration. In contrast to the state-of-the-art long reads error correction technique, which requires high computational resources and long running time on a supercomputer even for bacterial genome datasets, our software can produce comparable assembly using only a standard desktop in a short running time.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

"Holey Sheets" - Pfaffians and Subdeterminants as D-brane Operators in Large N Gauge Theories

In the AdS/CFT correspondence, wrapped D3-branes (such as "giant gravitons") on the string theory side of the correspondence have been identified with Pfaffian, determinant and subdeterminant operators on the field theory side. We substantiate this identification by showing that the presence of pairs of such operators in a correlation function of a large N gauge theory naturally leads to a modified 't Hooft expansion including also worldsheets with boundaries. This happens independently of supersymmetry or conformal invariance.Comment: 39 pages, 10 figures, harvma

LeakWatch: Estimating Information Leakage from Java Programs

Abstract. Programs that process secret data may inadvertently reveal information about those secrets in their publicly-observable output. This paper presents LeakWatch, a quantitative information leakage analysis tool for the Java programming language; it is based on a flexible “point-to-point ” information leakage model, where secret and publiclyobservable data may occur at any time during a program’s execution. LeakWatch repeatedly executes a Java program containing both secret and publicly-observable data and uses robust statistical techniques to provide estimates, with confidence intervals, for min-entropy leakage (using a new theoretical result presented in this paper) and mutual information. We demonstrate how LeakWatch can be used to estimate the size of information leaks in a range of real-world Java programs

Nariai, Bertotti-Robinson and anti-Nariai solutions in higher dimensions

We find all the higher dimensional solutions of the Einstein-Maxwell theory that are the topological product of two manifolds of constant curvature. These solutions include the higher dimensional Nariai, Bertotti-Robinson and anti-Nariai solutions, and the anti-de Sitter Bertotti-Robinson solutions with toroidal and hyperbolic topology (Plebanski-Hacyan solutions). We give explicit results for any dimension D>3. These solutions are generated from the appropriate extremal limits of the higher dimensional near-extreme black holes in a de Sitter, and anti-de Sitter backgrounds. Thus, we also find the mass and the charge parameters of the higher dimensional extreme black holes as a function of the radius of the degenerate horizon.Comment: 10 pages, 11 figures, RevTeX4. References added. Published versio

Thermodynamic and gravitational instability on hyperbolic spaces

We study the properties of anti--de Sitter black holes with a Gauss-Bonnet term for various horizon topologies (k=0, \pm 1) and for various dimensions, with emphasis on the less well understood k=-1 solution. We find that the zero temperature (and zero energy density) extremal states are the local minima of the energy for AdS black holes with hyperbolic event horizons. The hyperbolic AdS black hole may be stable thermodynamically if the background is defined by an extremal solution and the extremal entropy is non-negative. We also investigate the gravitational stability of AdS spacetimes of dimensions D>4 against linear perturbations and find that the extremal states are still the local minima of the energy. For a spherically symmetric AdS black hole solution, the gravitational potential is positive and bounded, with or without the Gauss-Bonnet type corrections, while, when k=-1, a small Gauss-Bonnet coupling, namely, \alpha << {l}^2 (where l is the curvature radius of AdS space), is found useful to keep the potential bounded from below, as required for stability of the extremal background.Comment: Shortened to match published (PRD) version, 18 pages, several eps figure

Current and Spin-Torque in Double Tunnel Barrier Ferromagnet - Superconductor - Ferromagnet Systems

We calculate the current and the spin-torque in small symmetric double tunnel barrier ferromagnet - superconductor - ferromagnet (F-S-F) systems. Spin-accumulation on the superconductor governs the transport properties when the spin-flip relaxation time is longer than the transport dwell time. In the elastic transport regime, it is demonstrated that the relative change in the current (spin-torque) for F-S-F systems equals the relative change in the current (spin-torque) for F-N-F systems upon changing the relative magnetization direction of the two ferromagnets. This differs from the results in the inelastic transport regime where spin-accumulation suppresses the superconducting gap and dramatically changes the magnetoresistance [S. Takahashi, H. Imamura, and S. Maekawa, Phys. Rev. Lett. 82, 3911 (1999)]. The experimental relevance of the elastic and inelastic transport regimes, respectively, as well as the reasons for the change in the transport properties are discussed.Comment: 7 page

Surface Terms as Counterterms in the AdS/CFT Correspondence

We examine the recently proposed technique of adding boundary counterterms to the gravitational action for spacetimes which are locally asymptotic to anti-de Sitter. In particular, we explicitly identify higher order counterterms, which allow us to consider spacetimes of dimensions d<=7. As the counterterms eliminate the need of ``background subtraction'' in calculating the action, we apply this technique to study examples where the appropriate background was ambiguous or unknown: topological black holes, Taub-NUT-AdS and Taub-Bolt-AdS. We also identify certain cases where the covariant counterterms fail to render the action finite, and we comment on the dual field theory interpretation of this result. In some examples, the case of vanishing cosmological constant may be recovered in a limit, which allows us to check results and resolve ambiguities in certain asymptotically flat spacetime computations in the literature.Comment: Revtex, 18 pages. References updated and few typo's fixed. Final versio

Charged AdS Black Holes and Catastrophic Holography

We compute the properties of a class of charged black holes in anti-de Sitter space-time, in diverse dimensions. These black holes are solutions of consistent Einstein-Maxwell truncations of gauged supergravities, which are shown to arise from the inclusion of rotation in the transverse space. We uncover rich thermodynamic phase structures for these systems, which display classic critical phenomena, including structures isomorphic to the van der Waals-Maxwell liquid-gas system. In that case, the phases are controlled by the universal `cusp' and `swallowtail' shapes familiar from catastrophe theory. All of the thermodynamics is consistent with field theory interpretations via holography, where the dual field theories can sometimes be found on the world volumes of coincident rotating branes.Comment: 19 pages, revtex, psfig, 6 multicomponent figures, typos, references and a few remarks have been repaired, and adde

Reissner-Nordstrom-de Sitter black hole, planar coordinates and dS/CFT

We discuss the Reissner-Nordstrom-de Sitter black holes in the context of dS/CFT correspondence by using static and planar coordinates. The boundary stress tensor and the mass of the solutions are computed. Also, we investigate how the RG flow is changed for different foliations. The Kastor-Traschen multi-black hole solution is considered as well as AdS counterparts of these configurations. In particular, we find that in planar coordinates the black holes appear like punctures in the dual boundary theory.Comment: 30 pages, 3 eps figures, JHEP style v2: new references added, misprints correcte