Catching homologies by geometric entropy

A geometric entropy is defined as the Riemannian volume of the parameter space of a statistical manifold associated with a given network. As such it can be a good candidate for measuring networks complexity. Here we investigate its ability to single out topological features of networks proceeding in a bottom-up manner: first we consider small size networks by analytical methods and then large size networks by numerical techniques. Two different classes of networks, the random graphs and the scale--free networks, are investigated computing their Betti numbers and then showing the capability of geometric entropy of detecting homologies.Comment: 12 pages, 2 Figure

A TDDFT study of the excited states of DNA bases and their assemblies

We present a detailed study of the optical absorption spectra of DNA bases and base pairs, carried out by means of time dependent density functional theory. The spectra for the isolated bases are compared to available theoretical and experimental data and used to assess the accuracy of the method and the quality of the exchange-correlation functional: Our approach turns out to be a reliable tool to describe the response of the nucleobases. Furthermore, we analyze in detail the impact of hydrogen bonding and $\pi$-stacking in the calculated spectra for both Watson-Crick base pairs and Watson-Crick stacked assemblies. We show that the reduction of the UV absorption intensity (hypochromicity) for light polarized along the base-pair plane depends strongly on the type of interaction. For light polarized perpendicular to the basal plane, the hypochromicity effect is reduced, but another characteristic is found, namely a blue shift of the optical spectrum of the base-assembly compared to that of the isolated bases. The use of optical tools as fingerprints for the characterization of the structure (and type of interaction) is extensively discussed.Comment: 31 pages, 8 figure

The Formation of non-Keplerian Rings of Matter about Compact Stars

The formation of energetic rings of matter in a Kerr spacetime with an outward pointing acceleration field does not appear to have previously been noted as a relativistic effect. In this paper we show that such rings are a gravimagneto effect with no Newtonian analog, and that they do not occur in the static limit. The energy efficiency of these rings can, depending of the strength of the acceleration field, be much greater than that of Keplerian disks. The rings rotate in a direction opposite to that of compact star about which they form. The size and energy efficiency of the rings depend on the fundamental parameters of the spacetime as well as the strength the acceleration field.Comment: 19 pages, 7 figures, 1 diagram. Figures are included in the text using the "graphicx" package. If you do not have this package you can use epsfig, or another package as long as you alter the tex file appropriately. Alternatively you could print the figures out seperatel

Structural fluctuations and quantum transport through DNA molecular wires: a combined molecular dynamics and model Hamiltonian approach

Charge transport through a short DNA oligomer (Dickerson dodecamer) in presence of structural fluctuations is investigated using a hybrid computational methodology based on a combination of quantum mechanical electronic structure calculations and classical molecular dynamics simulations with a model Hamiltonian approach. Based on a fragment orbital description, the DNA electronic structure can be coarse-grained in a very efficient way. The influence of dynamical fluctuations arising either from the solvent fluctuations or from base-pair vibrational modes can be taken into account in a straightforward way through time series of the effective DNA electronic parameters, evaluated at snapshots along the MD trajectory. We show that charge transport can be promoted through the coupling to solvent fluctuations, which gate the onsite energies along the DNA wire

Spinning test particles and clock effect in Kerr spacetime

We study the motion of spinning test particles in Kerr spacetime using the Mathisson-Papapetrou equations; we impose different supplementary conditions among the well known Corinaldesi-Papapetrou, Pirani and Tulczyjew's and analyze their physical implications in order to decide which is the most natural to use. We find that if the particle's center of mass world line, namely the one chosen for the multipole reduction, is a spatially circular orbit (sustained by the tidal forces due to the spin) then the generalized momentum $P$ of the test particle is also tangent to a spatially circular orbit intersecting the center of mass line at a point. There exists one such orbit for each point of the center of mass line where they intersect; although fictitious, these orbits are essential to define the properties of the spinning particle along its physical motion. In the small spin limit, the particle's orbit is almost a geodesic and the difference of its angular velocity with respect to the geodesic value can be of arbitrary sign, corresponding to the spin-up and spin-down possible alignment along the z-axis. We also find that the choice of the supplementary conditions leads to clock effects of substantially different magnitude. In fact, for co-rotating and counter-rotating particles having the same spin magnitude and orientation, the gravitomagnetic clock effect induced by the background metric can be magnified or inhibited and even suppressed by the contribution of the individual particle's spin. Quite surprisingly this contribution can be itself made vanishing leading to a clock effect undistiguishable from that of non spinning particles. The results of our analysis can be observationally tested.Comment: IOP macros, eps figures n. 12, to appear on Classical and Quantum Gravity, 200

A classification scheme for annotating speech acts in a business email corpus

This paper reports on the process of manual annotation of speech acts in a corpus of business emails, in the context of the PROBE project (PRagmatics of Business English). The project aims to bring together corpus, computational, and theoretical linguistics by drawing on the insights made available by the annotated corpus. The corpus data sheds light on the linguistic and discourse structures of speech act use in business email communication. This enhanced linguistic description can be compared to theoretical linguistic representations of speech act categories to assess how well traditional distinctions relate to real-world, naturally occurring data. From a computational perspective, the annotated data is required for the development of an automated speech act tagging tool. Central to this research is the creation of a high quality, manually annotated speech act corpus, using an easily interpretable classification scheme. We discuss the scheme chosen for the project and the training guidelines given to the annotators, and describe the main challenges identified by the annotators

Interpreting doubly special relativity as a modified theory of measurement

In this article we develop a physical interpretation for the deformed (doubly) special relativity theories (DSRs), based on a modification of the theory of measurement in special relativity. We suggest that it is useful to regard the DSRs as reflecting the manner in which quantum gravity effects induce Planck-suppressed distortions in the measurement of the "true" energy and momentum. This interpretation provides a framework for the DSRs that is manifestly consistent, non-trivial, and in principle falsifiable. However, it does so at the cost of demoting such theories from the level of "fundamental" physics to the level of phenomenological models -- models that should in principle be derivable from whatever theory of quantum gravity one ultimately chooses to adopt.Comment: 18 pages, plain LaTeX2

Dissipative Effects in the Electronic Transport through DNA Molecular Wires

We investigate the influence of a dissipative environment which effectively comprises the effects of counterions and hydration shells, on the transport properties of short \DNA wires. Their electronic structure is captured by a tight-binding model which is embedded in a bath consisting of a collection of harmonic oscillators. Without coupling to the bath a temperature independent gap opens in the electronic spectrum. Upon allowing for electron-bath interaction the gap becomes temperature dependent. It increases with temperature in the weak-coupling limit to the bath degrees of freedom. In the strong-coupling regime a bath-induced {\it pseudo-gap} is formed. As a result, a crossover from tunneling to activated behavior in the low-voltage region of the $I$-$V$ characteristics is observed with increasing temperature. The temperature dependence of the transmission near the Fermi energy, $t(E_{\rm F})$, manifests an Arrhenius-like behavior in agreement with recent transport experiments. Moreover, $t(E_{\rm F})$ shows a weak exponential dependence on the wire length, typical of strong incoherent transport. Disorder effects smear the electronic bands, but do not appreciably affect the pseudo-gap formation

An Anisotropic Wormhole:TUNNELLING in Time and Space

We discuss the structure of a gravitational euclidean instanton obtained through coupling of gravity to electromagnetism. Its topology at fixed $t$ is $S^1\times S^2$. This euclidean solution can be interpreted as a tunnelling to a hyperbolic space (baby universe) at $t=0$ or alternatively as a static wormhole that joins the two asymptotically flat spaces of a Reissner--Nordstr\"om type solution with $M=0$.Comment: PLAIN-TEX, 16 pages (4 figures not included), Report DFTT 2/9

Gyroscopic Precession and Inertial Forces in Axially Symmetric Stationary Spacetimes

We study the phenomenon of gyroscopic precession and the analogues of inertial forces within the framework of general relativity. Covariant connections between the two are established for circular orbits in stationary spacetimes with axial symmetry. Specializing to static spacetimes, we prove that gyroscopic precession and centrifugal force both reverse at the photon orbits. Simultaneous non-reversal of these in the case of stationary spacetimes is discussed. Further insight is gained in the case of static spacetime by considering the phenomena in a spacetime conformal to the original one. Gravi-electric and gravi-magnetic fields are studied and their relation to inertial forces is established.Comment: 21 pages, latex, no figures, http://202.41.67.76/~nayak/gpifass.te