Charge transport in poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers

We investigate the charge transport in synthetic DNA polymers built up from single types of base pairs. In the context of a polaron-like model, for which an electronic tight-binding system and bond vibrations of the double helix are coupled, we present estimates for the electron-vibration coupling strengths utilizing a quantum-chemical procedure. Subsequent studies concerning the mobility of polaron solutions, representing the state of a localized charge in unison with its associated helix deformation, show that the system for poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers, respectively possess quantitatively distinct transport properties. While the former supports unidirectionally moving electron breathers attributed to highly efficient long-range conductivity the breather mobility in the latter case is comparatively restrained inhibiting charge transport. Our results are in agreement with recent experimental results demonstrating that poly(dG)-poly(dC) DNA molecules acts as a semiconducting nanowire and exhibits better conductance than poly(dA)-poly(dT) ones.Comment: 11 pages, 5 figure

The interior of axisymmetric and stationary black holes: Numerical and analytical studies

We investigate the interior hyperbolic region of axisymmetric and stationary black holes surrounded by a matter distribution. First, we treat the corresponding initial value problem of the hyperbolic Einstein equations numerically in terms of a single-domain fully pseudo-spectral scheme. Thereafter, a rigorous mathematical approach is given, in which soliton methods are utilized to derive an explicit relation between the event horizon and an inner Cauchy horizon. This horizon arises as the boundary of the future domain of dependence of the event horizon. Our numerical studies provide strong evidence for the validity of the universal relation \Ap\Am = (8\pi J)^2 where \Ap and \Am are the areas of event and inner Cauchy horizon respectively, and $J$ denotes the angular momentum. With our analytical considerations we are able to prove this relation rigorously.Comment: Proceedings of the Spanish Relativity Meeting ERE 2010, 10 pages, 5 figure

Localization Properties of Electronic States in Polaron Model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers

We numerically investigate localization properties of electronic states in a static model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers with realistic parameters obtained by quantum-chemical calculation. The randomness in the on-site energies caused by the electron-phonon coupling are completely correlated to the off-diagonal parts. In the single electron model, the effect of the hydrogen-bond stretchings, the twist angles between the base pairs and the finite system size effects on the energy dependence of the localization length and on the Lyapunov exponent are given. The localization length is reduced by the influence of the fluctuations in the hydrogen bond stretchings. It is also shown that the helical twist angle affects the localization length in the poly(dG)-poly(dC) DNA polymer more strongly than in the poly(dA)-poly(dT) one. Furthermore, we show resonance structures in the energy dependence of the localization length when the system size is relatively small.Comment: 6 pages, 6 figure

Transport in Graphene: Ballistic or Diffusive?

We investigate the transport of electrons in disordered and pristine graphene devices. Fano shot noise, a standard metric to assess the mechanism for electronic transport in mesoscopic devices, has been shown to produce almost the same magnitude ($\approx 1/3$) in ballistic and diffusive graphene devices and is therefore of limited applicability. We consider a two-terminal geometry where the graphene flake is contacted by narrow metallic leads. We propose that the dependence of the conductance on the position of one of the leads, a conductance profile, can give us insight into the charge flow, which can in turn be used to analyze the transport mechanism. Moreover, we simulate scanning probe microscopy (SPM) measurements for the same devices, which can visualize the flow of charge inside the device, thus complementing the transport calculations. From our simulations, we find that both the conductance profile and SPM measurements are excellent tools to assess the transport mechanism differentiating ballistic and diffusive graphene systems.Comment: 11 pages, 7 figures. Renamed by editorial staff as "Ballistic versus diffusive transport in graphene

Causal Stability Ranking

Genotypic causes of a phenotypic trait are typically determined via randomized controlled intervention experiments. Such experiments are often prohibitive with respect to durations and costs. We therefore consider inferring stable rankings of genes, according to their causal effects on a phenotype, from observational data only. Our method allows for efficient design and prioritization of future experiments, and due to its generality it is useable for a broad spectrum of applications

Excitonic - vibronic coupled dimers: A dynamic approach

The dynamical properties of exciton transfer coupled to polarization vibrations in a two site system are investigated in detail. A fixed point analysis of the full system of Bloch - oscillator equations representing the coupled excitonic - vibronic flow is performed. For overcritical polarization a bifurcation converting the stable bonding ground state to a hyperbolic unstable state which is basic to the dynamical properties of the model is obtained. The phase space of the system is generally of a mixed type: Above bifurcation chaos develops starting from the region of the hyperbolic state and spreading with increasing energy over the Bloch sphere leaving only islands of regular dynamics. The behaviour of the polarization oscillator accordingly changes from regular to chaotic.Comment: uuencoded compressed Postscript file containing text and figures. In case of questions, please, write to [email protected]

Emerging Roles of Xenobiotic Detoxification Enzymes in Metabolic Diseases

Mammalian systems have developed extensive molecular mechanisms to protect against the toxicity of many exogenous xenobiotic compounds. Interestingly, many detoxification enzymes, including cytochrome P450s and flavin-containing monooxygenases, and their associated transcriptional activators [e.g. the aryl hydrocarbon receptor (AhR)], have now been shown to have endogenous roles in normal physiology and the pathology of metabolic diseases. This mini-review will focus on two such instances: the role of flavin-containing monooxygenase 3 (FMO3) in the formation of the cardiometabolic disease biomarker trimethylamine-N-oxide (TMAO) and the role of AhR as a sensor of endogenous ligands such as those generated by the gut microbiota. Understanding the roles of xenobiotic sensing pathways in endogenous metabolism will undoubtedly lead to a better understanding of how exposure to environmental pollutants can perturb these physiological processes