Electronic localization at mesoscopic length scales: different definitions of localization and contact effects in a heuristic DNA model

In this work we investigate the electronic transport along model DNA molecules using an effective tight-binding approach that includes the backbone on site energies. The localization length and participation number are examined as a function of system size, energy dependence, and the contact coupling between the leads and the DNA molecule. On one hand, the transition from an diffusive regime to a localized regime for short systems is identified, suggesting the necessity of a further length scale revealing the system borders sensibility. On the other hand, we show that the lenght localization and participation number, do not depended of system size and contact coupling in the thermodynamic limit. Finally we discuss possible length dependent origins for the large discrepancies among experimental results for the electronic transport in DNA sample

Pulsar Timing and its Application for Navigation and Gravitational Wave Detection

Pulsars are natural cosmic clocks. On long timescales they rival the precision of terrestrial atomic clocks. Using a technique called pulsar timing, the exact measurement of pulse arrival times allows a number of applications, ranging from testing theories of gravity to detecting gravitational waves. Also an external reference system suitable for autonomous space navigation can be defined by pulsars, using them as natural navigation beacons, not unlike the use of GPS satellites for navigation on Earth. By comparing pulse arrival times measured on-board a spacecraft with predicted pulse arrivals at a reference location (e.g. the solar system barycenter), the spacecraft position can be determined autonomously and with high accuracy everywhere in the solar system and beyond. We describe the unique properties of pulsars that suggest that such a navigation system will certainly have its application in future astronautics. We also describe the on-going experiments to use the clock-like nature of pulsars to "construct" a galactic-sized gravitational wave detector for low-frequency (f_GW ~1E-9 - 1E-7 Hz) gravitational waves. We present the current status and provide an outlook for the future.Comment: 30 pages, 9 figures. To appear in Vol 63: High Performance Clocks, Springer Space Science Review

Observing the First Stars and Black Holes

The high sensitivity of JWST will open a new window on the end of the cosmological dark ages. Small stellar clusters, with a stellar mass of several 10^6 M_sun, and low-mass black holes (BHs), with a mass of several 10^5 M_sun should be directly detectable out to redshift z=10, and individual supernovae (SNe) and gamma ray burst (GRB) afterglows are bright enough to be visible beyond this redshift. Dense primordial gas, in the process of collapsing from large scales to form protogalaxies, may also be possible to image through diffuse recombination line emission, possibly even before stars or BHs are formed. In this article, I discuss the key physical processes that are expected to have determined the sizes of the first star-clusters and black holes, and the prospect of studying these objects by direct detections with JWST and with other instruments. The direct light emitted by the very first stellar clusters and intermediate-mass black holes at z>10 will likely fall below JWST's detection threshold. However, JWST could reveal a decline at the faint-end of the high-redshift luminosity function, and thereby shed light on radiative and other feedback effects that operate at these early epochs. JWST will also have the sensitivity to detect individual SNe from beyond z=10. In a dedicated survey lasting for several weeks, thousands of SNe could be detected at z>6, with a redshift distribution extending to the formation of the very first stars at z>15. Using these SNe as tracers may be the only method to map out the earliest stages of the cosmic star-formation history. Finally, we point out that studying the earliest objects at high redshift will also offer a new window on the primordial power spectrum, on 100 times smaller scales than probed by current large-scale structure data.Comment: Invited contribution to "Astrophysics in the Next Decade: JWST and Concurrent Facilities", Astrophysics & Space Science Library, Eds. H. Thronson, A. Tielens, M. Stiavelli, Springer: Dordrecht (2008

Exact Hypersurface-Homogeneous Solutions in Cosmology and Astrophysics

A framework is introduced which explains the existence and similarities of most exact solutions of the Einstein equations with a wide range of sources for the class of hypersurface-homogeneous spacetimes which admit a Hamiltonian formulation. This class includes the spatially homogeneous cosmological models and the astrophysically interesting static spherically symmetric models as well as the stationary cylindrically symmetric models. The framework involves methods for finding and exploiting hidden symmetries and invariant submanifolds of the Hamiltonian formulation of the field equations. It unifies, simplifies and extends most known work on hypersurface-homogeneous exact solutions. It is shown that the same framework is also relevant to gravitational theories with a similar structure, like Brans-Dicke or higher-dimensional theories.Comment: 41 pages, REVTEX/LaTeX 2.09 file (don't use LaTeX2e !!!) Accepted for publication in Phys. Rev.

Phenomenology of the Lense-Thirring effect in the Solar System

Recent years have seen increasing efforts to directly measure some aspects of the general relativistic gravitomagnetic interaction in several astronomical scenarios in the solar system. After briefly overviewing the concept of gravitomagnetism from a theoretical point of view, we review the performed or proposed attempts to detect the Lense-Thirring effect affecting the orbital motions of natural and artificial bodies in the gravitational fields of the Sun, Earth, Mars and Jupiter. In particular, we will focus on the evaluation of the impact of several sources of systematic uncertainties of dynamical origin to realistically elucidate the present and future perspectives in directly measuring such an elusive relativistic effect.Comment: LaTex, 51 pages, 14 figures, 22 tables. Invited review, to appear in Astrophysics and Space Science (ApSS). Some uncited references in the text now correctly quoted. One reference added. A footnote adde

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Collapsing shear-free perfect fluid spheres with heat flow

A global view is given upon the study of collapsing shear-free perfect fluid spheres with heat flow. We apply a compact formalism, which simplifies the isotropy condition and the condition for conformal flatness. This formalism also presents the simplest possible version of the main junction condition, demonstrated explicitly for conformally flat and geodesic solutions. It gives the right functions to disentangle this condition into well known differential equations like those of Abel, Riccati, Bernoulli and the linear one. It yields an alternative derivation of the general solution with functionally dependent metric components. We bring together the results for static and time- dependent models to describe six generating functions of the general solution to the isotropy equation. Their common features and relations between them are elucidated. A general formula for separable solutions is given, incorporating collapse to a black hole or to a naked singularity.Comment: 26 page

Constraining the electric charges of some astronomical bodies in Reissner-Nordstrom spacetimes and generic r^-2-type power-law potentials from orbital motions

We put model-independent, dynamical constraints on the net electric charge Q of some astronomical and astrophysical objects by assuming that their exterior spacetimes are described by the Reissner-Nordstroem metric, which induces an additional potential U_RN \propto Q^2 r^-2. Our results extend to other hypothetical power-law interactions inducing extra-potentials U_pert = r^-2 as well (abridged).Comment: LaTex2e, 16 pages, 3 figures, no tables, 128 references. Version matching the one at press in General Relativity and Gravitation (GRG). arXiv admin note: substantial text overlap with arXiv:1112.351

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy