Two-level system with a thermally fluctuating transfer matrix element: Application to the problem of DNA charge transfer

Charge transfer along the base-pair stack in DNA is modeled in terms of thermally-assisted tunneling between adjacent base pairs. Central to our approach is the notion that tunneling between fluctuating pairs is rate-limited by the requirement of their optimal alignment. We focus on this aspect of the process by modeling two adjacent base pairs in terms of a classical damped oscillator subject to thermal fluctuations as described by a Fokker-Planck equation. We find that the process is characterized by two time scales, a result that is in accord with experimental findings.Comment: original file is revtex4, 10 pages, three eps figure

Polarons with a twist

We consider a polaron model where molecular \emph{rotations} are important. Here, the usual hopping between neighboring sites is affected directly by the electron-phonon interaction via a {\em twist-dependent} hopping amplitude. This model may be of relevance for electronic transport in complex molecules and polymers with torsional degrees of freedom, such as DNA, as well as in molecular electronics experiments where molecular twist motion is significant. We use a tight-binding representation and find that very different polaronic properties are already exhibited by a two-site model -- these are due to the nonlinearity of the restoring force of the twist excitations, and of the electron-phonon interaction in the model. In the adiabatic regime, where electrons move in a {\em low}-frequency field of twisting-phonons, the effective splitting of the energy levels increases with coupling strength. The bandwidth in a long chain shows a power-law suppression with coupling, unlike the typical exponential dependence due to linear phonons.Comment: revtex4 source and one eps figur

A Kinematically Complete Measurement of the Proton Structure Function F2 in the Resonance Region and Evaluation of Its Moments

We measured the inclusive electron-proton cross section in the nucleon resonance region (W < 2.5 GeV) at momentum transfers Q**2 below 4.5 (GeV/c)**2 with the CLAS detector. The large acceptance of CLAS allowed for the first time the measurement of the cross section in a large, contiguous two-dimensional range of Q**2 and x, making it possible to perform an integration of the data at fixed Q**2 over the whole significant x-interval. From these data we extracted the structure function F2 and, by including other world data, we studied the Q**2 evolution of its moments, Mn(Q**2), in order to estimate higher twist contributions. The small statistical and systematic uncertainties of the CLAS data allow a precise extraction of the higher twists and demand significant improvements in theoretical predictions for a meaningful comparison with new experimental results.Comment: revtex4 18 pp., 12 figure

Green function techniques in the treatment of quantum transport at the molecular scale

The theoretical investigation of charge (and spin) transport at nanometer length scales requires the use of advanced and powerful techniques able to deal with the dynamical properties of the relevant physical systems, to explicitly include out-of-equilibrium situations typical for electrical/heat transport as well as to take into account interaction effects in a systematic way. Equilibrium Green function techniques and their extension to non-equilibrium situations via the Keldysh formalism build one of the pillars of current state-of-the-art approaches to quantum transport which have been implemented in both model Hamiltonian formulations and first-principle methodologies. We offer a tutorial overview of the applications of Green functions to deal with some fundamental aspects of charge transport at the nanoscale, mainly focusing on applications to model Hamiltonian formulations.Comment: Tutorial review, LaTeX, 129 pages, 41 figures, 300 references, submitted to Springer series "Lecture Notes in Physics

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

Tensor Polarization of the phi meson Photoproduced at High t

As part of a measurement of the cross section of $\phi$ meson photoproduction to high momentum transfer, we measured the polar angular decay distribution of the outgoing $K^+$ in the channel $\phi \to K^+K^-$ in the $\phi$ center-of-mass frame (the helicity frame). We find that s-channel helicity conservation (SCHC) holds in the kinematical range where $t$-channel exchange dominates (up to $-t \sim 2.5$ GeV$^2$ for $E_{\gamma}$=3.6 GeV). Above this momentum, $u$-channel production of a $\phi$ meson dominates and induces a violation of SCHC. The deduced value of the $\phi NN$ coupling constant lies in the upper range of previously reported values.Comment: 6 pages; 5 figure

Exclusive ρ0\rho^0 meson electroproduction from hydrogen at CLAS

The longitudinal and transverse components of the cross section for the $e p\to e^\prime p \rho^0$ reaction were measured in Hall B at Jefferson Laboratory using the CLAS detector. The data were taken with a 4.247 GeV electron beam and were analyzed in a range of $x_B$ from 0.2 to 0.6 and of $Q^2$ from 1.5 to 3.0 GeV$^2$. The data are compared to a Regge model based on effective hadronic degrees of freedom and to a calculation based on Generalized Parton Distributions. It is found that the transverse part of the cross section is well described by the former approach while the longitudinal part can be reproduced by the latter.Comment: 6 pages, 4 figure

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

Search for jet extinction in the inclusive jet-pT spectrum from proton-proton collisions at s=8 TeV

Published by the American Physical Society under the terms of the Creative Commons Attribution 3.0 License. Further distribution of this work must maintain attribution to the author(s) and the published articles title, journal citation, and DOI.The first search at the LHC for the extinction of QCD jet production is presented, using data collected with the CMS detector corresponding to an integrated luminosity of 10.7  fb−1 of proton-proton collisions at a center-of-mass energy of 8 TeV. The extinction model studied in this analysis is motivated by the search for signatures of strong gravity at the TeV scale (terascale gravity) and assumes the existence of string couplings in the strong-coupling limit. In this limit, the string model predicts the suppression of all high-transverse-momentum standard model processes, including jet production, beyond a certain energy scale. To test this prediction, the measured transverse-momentum spectrum is compared to the theoretical prediction of the standard model. No significant deficit of events is found at high transverse momentum. A 95% confidence level lower limit of 3.3 TeV is set on the extinction mass scale

The Great Markarian 421 Flare of 2010 February: Multiwavelength Variability and Correlation Studies

We report on variability and correlation studies using multiwavelength observations of the blazar Mrk 421 during the month of 2010 February, when an extraordinary flare reaching a level of ∼27 Crab Units above 1 TeV was measured in very high energy (VHE) γ-rays with the Very Energetic Radiation Imaging Telescope Array System (VERITAS) observatory. This is the highest flux state for Mrk 421 ever observed in VHE γ-rays. Data are analyzed from a coordinated campaign across multiple instruments, including VHE γ-ray (VERITAS, Major Atmospheric Gamma-ray Imaging Cherenkov), high-energy γ-ray (Fermi-LAT), X-ray (Swift, Rossi X-ray Timing Experiment, MAXI), optical (including the GASP-WEBT collaboration and polarization data), and radio (Metsahovi, Owens Valley Radio Observatory, University of Michigan Radio Astronomy Observatory). Light curves are produced spanning multiple days before and after the peak of the VHE flare, including over several flare "decline" epochs. The main flare statistics allow 2 minute time bins to be constructed in both the VHE and optical bands enabling a cross-correlation analysis that shows evidence for an optical lag of ∼25-55 minutes, the first time-lagged correlation between these bands reported on such short timescales. Limits on the Doppler factor (δ ⪆ 33) and the size of the emission region (δ-1RB≲ 3.8 × 1013cm) are obtained from the fast variability observed by VERITAS during the main flare. Analysis of 10 minute binned VHE and X-ray data over the decline epochs shows an extraordinary range of behavior in the flux-flux relationship, from linear to quadratic to lack of correlation to anticorrelation. Taken together, these detailed observations of an unprecedented flare seen in Mrk 421 are difficult to explain with the classic single-zone synchrotron self-Compton model.</p