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

Entropy of Lovelock Black Holes

A general formula for the entropy of stationary black holes in Lovelock gravity theories is obtained by integrating the first law of black hole mechanics, which is derived by Hamiltonian methods. The entropy is not simply one quarter of the surface area of the horizon, but also includes a sum of intrinsic curvature invariants integrated over a cross section of the horizon.Comment: 15 pages, plain Latex, NSF-ITP-93-4

Rational foundation of GR in terms of statistical mechanic in the AdS/CFT framework

In this article, we work out the microscopic statistical foundation of the supergravity description of the simplest 1/2 BPS sector in the AdS(5)/CFT(4). Then, all the corresponding supergravity observables are related to thermodynamical observables, and General Relativity is understood as a mean-field theory. In particular, and as an example, the Superstar is studied and its thermodynamical properties clarified.Comment: 13 pages, 6 eps figures, latex, some improvements introduced, reference added, typos correcte

Gravitation with superposed Gauss--Bonnet terms in higher dimensions: Black hole metrics and maximal extensions

Our starting point is an iterative construction suited to combinatorics in arbitarary dimensions d, of totally anisymmetrised p-Riemann 2p-forms (2p\le d) generalising the (1-)Riemann curvature 2-forms. Superposition of p-Ricci scalars obtained from the p-Riemann forms defines the maximally Gauss--Bonnet extended gravitational Lagrangian. Metrics, spherically symmetric in the (d-1) space dimensions are constructed for the general case. The problem is directly reduced to solving polynomial equations. For some black hole type metrics the horizons are obtained by solving polynomial equations. Corresponding Kruskal type maximal extensions are obtained explicitly in complete generality, as is also the periodicity of time for Euclidean signature. We show how to include a cosmological constant and a point charge. Possible further developments and applications are indicated.Comment: 13 pages, REVTEX. References and Note Adde

Fermions from Half-BPS Supergravity

We discuss collective coordinate quantization of the half-BPS geometries of Lin, Lunin and Maldacena (hep-th/0409174). The LLM geometries are parameterized by a single function $u$ on a plane. We treat this function as a collective coordinate. We arrive at the collective coordinate action as well as path integral measure by considering D3 branes in an arbitrary LLM geometry. The resulting functional integral is shown, using known methods (hep-th/9309028), to be the classical limit of a functional integral for free fermions in a harmonic oscillator. The function $u$ gets identified with the classical limit of the Wigner phase space distribution of the fermion theory which satisfies u * u = u. The calculation shows how configuration space of supergravity becomes a phase space (hence noncommutative) in the half-BPS sector. Our method sheds new light on counting supersymmetric configurations in supergravity.Comment: 28 pages, 2 figures, epsf;(v3) eq. (3.3) clarified and notationally simplified; version to appear in JHE

New supersymmetric solutions of N=2, D=5 gauged supergravity with hyperscalars

We construct new supersymmetric solutions, including AdS bubbles, in an N=2 truncation of five-dimensional N=8 gauged supergravity. This particular truncation is given by N=2 gauged supergravity coupled to two vector multiples and three incomplete hypermultiplets, and was originally investigated in the context of obtaining regular AdS bubble geometries with multiple active R-charges. We focus on cohomogeneity-one solutions corresponding to objects with two equal angular momenta and up to three independent R-charges. Curiously, we find a new set of zero and negative mass solitons asymptotic to AdS_5/Z_k, for k \ge 3, which are everywhere regular without closed timelike curves.Comment: Latex 3 times, 42 page

Singularities and closed time-like curves in type IIB 1/2 BPS geometries

We study in detail the moduli space of solutions discovered in LLM relaxing the constraint that guarantees the absence of singularities. The solutions fall into three classes, non-singular, null-singular and time machines with a time-like naked singularity. We study the general features of these metrics and prove that there are actually just two generic classes of space-times - those with null singularities are in the same class as the non-singular metrics. AdS/CFT seems to provide a dual description only for the first of these two types of space-time in terms of a unitary CFT indicating the possible existence of a chronology protection mechanism for this class of geometries.Comment: 34 pages, 7 figures, LaTeX. References adde

Black strings in asymptotically plane wave geometries

We present a class of black string spacetimes which asymptote to maximally symmetric plane wave geometries. Our construction will rely on a solution generating technique, the null Melvin twist, which deforms an asymptotically flat black string spacetime to an asymptotically plane wave black string spacetime while preserving the event horizon.Comment: 15 pages; references adde

Giant gravitons in AdS/CFT (I): matrix model and back reaction

In this article we study giant gravitons in the framework of AdS/CFT correspondence. First, we show how to describe these configurations in the CFT side using a matrix model. In this picture, giant gravitons are realized as single excitations high above a Fermi sea, or as deep holes into it. Then, we give a prescription to define quasi-classical states and we recover the known classical solution associated to the CFT dual of a giant graviton that grows in AdS. Second, we use the AdS/CFT dictionary to obtain the supergravity boundary stress tensor of a general state and to holographically reconstruct the bulk metric, obtaining the back reaction of space-time. We find that the space-time response to all the supersymmetric giant graviton states is of the same form, producing the singular BPS limit of the three charge Reissner-Nordstr\"om-AdS black holes. While computing the boundary stress tensor, we comment on the finite counterterm recently introduced by Liu and Sabra, and connect it to a scheme-dependent conformal anomaly.Comment: 28 pages, JHEP3 class. v2: typos corrected and references adde

Geometrothermodynamics of five dimensional black holes in Einstein-Gauss-Bonnet-theory

We investigate the thermodynamic properties of 5D static and spherically symmetric black holes in (i) Einstein-Maxwell-Gauss-Bonnet theory, (ii) Einstein-Maxwell-Gauss-Bonnet theory with negative cosmological constant, and in (iii) Einstein-Yang-Mills-Gauss-Bonnet theory. To formulate the thermodynamics of these black holes we use the Bekenstein-Hawking entropy relation and, alternatively, a modified entropy formula which follows from the first law of thermodynamics of black holes. The results of both approaches are not equivalent. Using the formalism of geometrothermodynamics, we introduce in the manifold of equilibrium states a Legendre invariant metric for each black hole and for each thermodynamic approach, and show that the thermodynamic curvature diverges at those points where the temperature vanishes and the heat capacity diverges.Comment: New sections added, references adde