Scalar Field Inhomogeneous Cosmologies

Some exact solutions for the Einstein field equations corresponding to inhomogeneous $G_2$ cosmologies with an exponential-potential scalar field which generalize solutions obtained previously are considered. Several particular cases are studied and the properties related to generalized inflation and asymptotic behaviour of the models are discussed.Comment: 21 pages LaTeX, 3 figures appended as a uuencoded compressed tar fil

Penrose Limits, the Colliding Plane Wave Problem and the Classical String Backgrounds

We show how the Szekeres form of the line element is naturally adapted to study Penrose limits in classical string backgrounds. Relating the "old" colliding wave problem to the Penrose limiting procedure as employed in string theory we discuss how two orthogonal Penrose limits uniquely determine the underlying target space when certain symmetry is imposed. We construct a conformally deformed background with two distinct, yet exactly solvable in terms of the string theory on R-R backgrounds, Penrose limits. Exploiting further the similarities between the two problems we find that the Penrose limit of the gauged WZW Nappi-Witten universe is itself a gauged WZW plane wave solution of Sfetsos and Tseytlin. Finally, we discuss some issues related to singularity, show the existence of a large class of non-Hausdorff solutions with Killing Cauchy Horizons and indicate a possible resolution of the problem of the definition of quantum vacuum in string theory on these time-dependent backgrounds.Comment: Some misprints corrected. Matches the version in print. To appear in Classical & Quantum Gravit

Power-law expansion in k-essence cosmology

We study spatially flat isotropic universes driven by k-essence. It is shown that Friedmann and k-field equations may be analytically integrated for arbitrary k-field potentials during evolution with a constant baryotropic index. It follows that there is an infinite number of dynamically different k-theories with equivalent kinematics of the gravitational field. We show that there is a large "window" of stable solutions, and that the dust-like behaviour separates stable from unstable expansion. Restricting to the family of power law solutions, it is argued that the linear scalar field model, with constant function F, is isomorphic to a model with divergent speed of sound and this makes them less suitable for cosmological modeling than the non-linear k-field solutions we find in this paper.Comment: Revised version. A detailed discussion relating the power-law solutions with the linear K-essence field and inverse square potential, on one hand, and the models with divergent sound volocity, on the other, is adde

EFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands

Molecular structures and functions of the majority of proteins across different species are yet to be identified. Much needed functional annotation of these gene products often benefits from the knowledge of protein-ligand interactions. Towards this goal, we developed eFindSite, an improved version of FINDSITE, designed to more efficiently identify ligand binding sites and residues using only weakly homologous templates. It employs a collection of effective algorithms, including highly sensitive meta-threading approaches, improved clustering techniques, advanced machine learning methods and reliable confidence estimation systems. Depending on the quality of target protein structures, eFindSite outperforms geometric pocket detection algorithms by 15-40 % in binding site detection and by 5-35 % in binding residue prediction. Moreover, compared to FINDSITE, it identifies 14 % more binding residues in the most difficult cases. When multiple putative binding pockets are identified, the ranking accuracy is 75-78 %, which can be further improved by 3-4 % by including auxiliary information on binding ligands extracted from biomedical literature. As a first across-genome application, we describe structure modeling and binding site prediction for the entire proteome of Escherichia coli. Carefully calibrated confidence estimates strongly indicate that highly reliable ligand binding predictions are made for the majority of gene products, thus eFindSite holds a significant promise for large-scale genome annotation and drug development projects. eFindSite is freely available to the academic community at http://www.brylinski.org/efindsite. © 2013 Springer Science+Business Media Dordrecht

Long-Term Optical Monitoring of Eta Carinae. Multiband light curves for a complete orbital period

The periodicity of 5.5 years for some observational events occurring in Eta Carinae manifests itself across a large wavelength range and has been associated with its binary nature. These events are supposed to occur when the binary components are close to periastron. To detect the previous periastron passage of Eta Car in 2003, we started an intensive, ground-based, optical, photometric observing campaign. We continued observing the object to monitor its photometric behavior and variability across the entire orbital cycle. Our observation program consisted of daily differential photometry from CCD images, which were acquired using a 0.8 m telescope and a standard BVRI filter set at La Plata Observatory. The photometry includes the central object and the surrounding Homunculus nebula. We present up-to-date results of our observing program, including homogeneous photometric data collected between 2003 and 2008. Our observations demonstrated that Eta Car has continued increasing in brightness at a constant rate since 1998. In 2006, it reached its brightest magnitude (V ~ 4.7) since about 1860s. The object then suddenly reverted its brightening trend, fading to V = 5.0 at the beginning of 2007, and has maintained a quite steady state since then. We continue the photometric monitoring of Eta Car in anticipation of the next "periastron passage", predicted to occur at the beginning of 2009.Comment: Accepted by A&A. The paper contains 3 figures and 2 table

An unusual initial presentation of mantle cell lymphoma arising from the lymphoid stroma of warthin tumor.

BackgroundWarthin tumors presenting concomitantly with a lymphoma is vanishingly rare with only 15 reported cases in English literature. Herein, we report an unusual initial presentation of a mantle cell lymphoma involving the lymphoid stroma of a Warthin tumor.Case presentationA seventy-seven year old otherwise healthy gentleman with a 50-pack year smoking history presents with a slowly enlarging left cheek mass. CT scan of the neck demonstrated a left parotid gland tumor measuring 3.4 cm in greatest dimension. He underwent a left superficial parotidectomy, with subsequent histopathologic examination revealing a Warthin tumor with extensive expansion of the lymphoid stroma. Flow cytometric, immunohistochemical, and cytogenetic studies of the stromal component of the tumor confirmed the presence of a mantle cell lymphoma. Clinical staging demonstrated stage IVa disease, and was considered to be at low to intermediate risk due to the slow growth of the parotid lesion. The patient is undergoing close follow up with repeat PET-CT scans at six months.ConclusionTo the best of our knowledge, this is the first well documented collision tumor between mantle cell lymphoma and a Warthin tumor. This case also brings to light the significance of thorough evaluation of the lymphoid component of Warthin tumor

Initial Conditions and the Structure of the Singularity in Pre-Big-Bang Cosmology

We propose a picture, within the pre-big-bang approach, in which the universe emerges from a bath of plane gravitational and dilatonic waves. The waves interact gravitationally breaking the exact plane symmetry and lead generically to gravitational collapse resulting in a singularity with the Kasner-like structure. The analytic relations between the Kasner exponents and the initial data are explicitly evaluated and it is shown that pre-big-bang inflation may occur within a dense set of initial data. Finally, we argue that plane waves carry zero gravitational entropy and thus are, from a thermodynamical point of view, good candidates for the universe to emerge from.Comment: 18 pages, LaTeX, epsfig. 3 figures included. Minor changes; paragraph added in the introduction, references added and typos corrected. Final version published in Classical and Quantum Gravit

Gravitational Optics: Self-phase modulation and harmonic cascades

Nonlinear wave interaction of low amplitude gravitational waves in flat space-time is considered. Analogy with optics is established. It is shown that the flat metric space-time is equivalent to a centro-symmetric optical medium, with no second order susceptibility. The lowest order nonlinear effects are those due to the third order nonlinearity and include self-phase modulation and high harmonic generation. These processes lead to an efficient energy dilution of the gravitational wave energy over an increasingly large spectral range.Comment: 12 pages, REVTEX

Accelerating the pace of protein functional annotation with intel xeon phi coprocessors

© 2002-2011 IEEE. Intel Xeon Phi is a new addition to the family of powerful parallel accelerators. The range of its potential applications in computationally driven research is broad; however, at present, the repository of scientific codes is still relatively limited. In this study, we describe the development and benchmarking of a parallel version of {\mmb e}FindSite, a structural bioinformatics algorithm for the prediction of ligand-binding sites in proteins. Implemented for the Intel Xeon Phi platform, the parallelization of the structure alignment portion of {\mmb e}FindSite using pragma-based OpenMP brings about the desired performance improvements, which scale well with the number of computing cores. Compared to a serial version, the parallel code runs 11.8 and 10.1 times faster on the CPU and the coprocessor, respectively; when both resources are utilized simultaneously, the speedup is 17.6. For example, ligand-binding predictions for 501 benchmarking proteins are completed in 2.1 hours on a single Stampede node equipped with the Intel Xeon Phi card compared to 3.1 hours without the accelerator and 36.8 hours required by a serial version. In addition to the satisfactory parallel performance, porting existing scientific codes to the Intel Xeon Phi architecture is relatively straightforward with a short development time due to the support of common parallel programming models by the coprocessor. The parallel version of {\mmb e}FindSite is freely available to the academic community at www.brylinski.org/efindsite