On the Deactivation Mechanisms of Adenine-Thymine Base Pair

In this contribution, the multiconfigurational second-order perturbation theory method based on a complete active space reference wave function (CASSCF/CASPT2) is applied to study all possible single and double proton/hydrogen transfers between the nucleobases in the adenine-thymine (AT) base pair, analyzing the role of excited states with different nature [localized (LE) and charge transfer (CT)] and considering concerted as well as step-wise mechanisms. According to the findings, once the lowest excited states, localized in adenine, are populated during UV irradiation of the Watson-Crick base pair, the proton transfer in the N-O bridge does not require high energy in order to populate a CT state. The latter state will immediately relax toward a crossing with the ground state, which will funnel the system to either the canonical structure or the imino-enol tautomer. The base pair is also capable of repairing itself easily since the imino-enol species is unstable to thermal conversion.

Pair approximation for a model of vertical and horizontal transmission of parasites.

We apply Stochastic Dynamics method for a differential equations model, proposed by Marc Lipsitch and collaborators (Proc. R. Soc. Lond. B 260, 321, 1995), for which the transmission dynamics of parasites occurs from a parent to its offspring (vertical transmission), and by contact with infected host (horizontal transmission). Herpes, Hepatitis and AIDS are examples of diseases for which both horizontal and vertical transmission occur simultaneously during the virus spreading. Understanding the role of each type of transmission in the infection prevalence on a susceptible host population may provide some information about the factors that contribute for the eradication and/or control of those diseases. We present a pair mean-field approximation obtained from the master equation of the model. The pair approximation is formed by the differential equations of the susceptible and infected population densities and the differential equations of pairs that contribute to the former ones. In terms of the model parameters, we obtain the conditions that lead to the disease eradication, and set up the phase diagram based on the local stability analysis of fixed points. We also perform Monte Carlo simulations of the model on complete graphs and Erdös-Rényi graphs in order to investigate the influence of population size and neighborhood on the previous mean-field results; by this way, we also expect to evaluate the contribution of vertical and horizontal transmission on the elimination of parasite. Pair Approximation for a Model of Vertical and Horizontal Transmission of Parasites.

A Sib-Pair analysis of impulsivity in bipolar disorder type I

OBJECTIVE: The aim of this study was to compare impulsivity among patients with bipolar disorder, their siblings, and healthy controls in order to examine whether impulsivity in bipolar disorder is related to genetic liability for the illness. METHODS: Using the Barratt Impulsiveness Scale, we assessed 204 subjects: 67 euthymic outpatients with bipolar disorder type I, 67 siblings without bipolar disorder, and 70 healthy controls. RESULTS: Impulsivity scores were higher among patients with bipolar disorder than among healthy controls. Siblings showed higher motor impulsivity scores than did healthy controls. CONCLUSIONS: Our results suggest that motor impulsivity may be a vulnerability marker for bipolar disorder. Our data may contribute to further improve preventive strategies in subjects at high risk for bipolar disorder.

Two-degree-of-freedom vortex-induced vibration of circular cylinders with very low aspect ratio and small mass ratio

The investigation of vortex-induced vibration on very short cylinders with two degrees of freedom has drawn the attention of a large number of researchers. Some investigations on such a problem are carried out in order to have a better understanding of the physics involved in vortex-induced motions of floating bodies such as offshore platforms. In this paper, experiments were carried out in a recirculating water channel over the range of Reynolds number 6000

One and two degrees-of-freedom Vortex-Induced Vibration experiments with yawed cylinders

Vortex-Induced Vibration (VIV) experiments were carried out with yawed cylinders. The purpose was to investigate the validity of the Independence Principle (IP) for properly describing the flow characteristics and the dynamics of structures subjected to oblique flow. Five yaw angles in relation to the direction perpendicular to the free stream velocity were tested, namely View the MathML sourceθ=0°,10°,20°,30° and 45°. Both the upstream and downstream orientations were tested. The models were mounted on a leaf spring apparatus that allows experiments with one or two degrees of freedom. The Reynolds numbers based on the component normal to the cylinder axis fell in the interval 3×103

The role of wake stiffness on the wake-induced vibration of the downstream cylinder of a tandem pair

When a pair of tandem cylinders is immersed in a flow the downstream cylinder can be excited into wake-induced vibrations (WIV) due to the interaction with vortices coming from the upstream cylinder. Assi, Bearman & Meneghini ( J. Fluid Mech. , vol. 661, 2010, pp. 365–401) concluded that the WIV excitation mechanism has its origin in the unsteady vortex–structure interaction encountered by the cylinder as it oscillates across the wake. In the present paper we investigate how the cylinder responds to that excitation, characterising the amplitude and frequency of response and its dependency on other parameters of the system. We introduce the concept of wake stiffness , a fluid dynamic effect that can be associated, to a first approximation, with a linear spring with stiffness proportional to Re and to the steady lift force occurring for staggered cylinders. By a series of experiments with a cylinder mounted on a base without springs we verify that such wake stiffness is not only strong enough to sustain oscillatory motion, but can also dominate over the structural stiffness of the system. We conclude that while unsteady vortex–structure interactions provide the energy input to sustain the vibrations, it is the wake stiffness phenomenon that defines the character of the WIV response

Two-degree-of-freedom vortex-induced vibration of circular cylinders with very low aspect ratio and small mass ratio

The investigation of vortex-induced vibration on very short cylinders with two degrees of freedom has drawn the attention of a large number of researchers. Some investigations on such a problem are carried out in order to have a better understanding of the physics involved in vortex-induced motions of floating bodies such as offshore platforms. In this paper, experiments were carried out in a recirculating water channel over the range of Reynolds number 6000

3-D geometry reconstruction using a color image stereo pair and partial differential equations

[EN] In this work, we present a new model for a dense disparity estimation and the 3-D geometry reconstruction using a color image stereo pair. First, we present a brief introduction to the 3-D Geometry of a camera system. Next, we propose a new model for the disparity estimation based on an energy functional. We look for the local minima of the energy using the associate Euler-Langrage partial differential equations. This model is a generalization to color image of the model developed in, with some changes in the strategy to avoid the irrelevant local minima. We present some numerical experiences of 3-D reconstruction, using this method some real stereo pairs.

Potential vorticity conserving flows and vortex-wave interaction : the role of vertical velocity and isopycnal diffusion on plankton heterogeneity

Programa de doctorado de oceanografía

Diagnostic techniques for EHD and MHD interaction

The impact of plasma technologies is growing both in the academic and in the industrial fields. Nowadays, a great interest is focused in plasma applications in aeronautics and astronautics domains. Plasma actuators based on the Magneto-Hydro-Dynamic (MHD) and Electro- Hydro-Dynamic (EHD) interactions are potentially able to suitably modify the fluid-dynamics characteristics around a flying body without utilizing moving parts. This could lead to the control of an aircraft with negligible response time, more reliability and improvements of the performance. In order to study the aforementioned interactions, a series of experiments and a wide number of diagnostic techniques have been utilized. The EHD interaction, realized by means of a Dielectric Barrier Discharge (DBD) actuator, and its impact on the boundary layer have been evaluated by means of two different experiments. In the first one a three phase multi-electrode flat panel actuator is used. Different external flow velocities (from 1 to 20m/s) and different values of the supplied voltage and frequency have been considered. Moreover a change of the phase sequence has been done to verify the influence of the electric field existing between successive phases. Measurements of the induced speed had shown the effect of the supply voltage and the frequency, and the phase order in the momentum transfer phenomenon. Gains in velocity, inside the boundary layer, of about 5m/s have been obtained. Spectroscopic measurements allowed to determine the rotational and the vibrational temperature of the plasma which lie in the range of 320 ÷ 440°K and of 3000 ÷ 3900°K respectively. A deviation from thermodynamic equilibrium had been found. The second EHD experiment is realized on a single electrode pair DBD actuator driven by nano-pulses superimposed to a DC or an AC bias. This new supply system separates the plasma formation mechanism from the acceleration action on the fluid, leading to an higher degree of the control of the process. Both the voltage and the frequency of the nano-pulses and the amplitude and the waveform of the bias have been varied during the experiment. Plasma jets and vortex behavior had been observed by means of fast Schlieren imaging. This allowed a deeper understanding of the EHD interaction process. A velocity increase in the boundary layer of about 2m/s had been measured. Thrust measurements have been performed by means of a scales and compared with experimental data reported in the literature. For similar voltage amplitudes thrust larger than those of the literature, had been observed. Surface charge measurements led to realize a modified DBD actuator able to obtain similar performances when compared with that of other experiments. However in this case a DC bias replacing the AC bias had been used. MHD interaction experiments had been carried out in a hypersonic wind tunnel in argon with a flow of Mach 6. Before the MHD experiments a thermal, fluid-dynamic and plasma characterization of the hypersonic argon plasma flow have been done. The electron temperature and the electron number density had been determined by means of emission spectroscopy and microwave absorption measurements. A deviation from thermodynamic equilibrium had been observed. The electron number density showed to be frozen at the stagnation region condition in the expansion through the nozzle. MHD experiments have been performed using two axial symmetric test bodies. Similar magnetic configurations were used. Permanent magnets inserted into the test body allowed to generate inside the plasma azimuthal currents around the conical shape of the body. These Faraday currents are responsible of the MHD body force which acts against the flow. The MHD interaction process has been observed by means of fast imaging, pressure and electrical measurements. Images showed bright rings due to the Faraday currents heating and exciting the plasma particles. Pressure measurements showed increases of the pressure in the regions where the MHD interaction is large. The pressure is 10 to 15% larger than when the MHD interaction process is silent. Finally by means of electrostatic probes mounted flush on the test body lateral surface Hall fields of about 500V/m had been measured. These results have been used for the validation of a numerical MHD code.

Vortex dynamics in the high-temperature superconductors YBa 2 Cu 3 O 7 and Bi 2 Sr 2 CaCu 2 O 8 + delta in low- and high-dissipative transport measurements

This thesis investigates phenomena of vortex dynamics in type II superconductors depending on the dimensionality of the flux-line system and the strength of the driving force. In the low dissipative regime of Bi_2Sr_2CaCu_2O_{8+delta} (BSCCO) the influence of oxygen stoichiometry on flux-line tension was examined. An entanglement crossover of the vortex system at low magnetic fields was identified and a comprehensive B-T phase diagram of solid and fluid phases derived.In YBa_2Cu_3O_7 (YBCO) extremely long (>100 mm) high-quality measurement bridges allowed to extend the electric-field window in transport measurements by up to three orders of magnitude. Complementing analyses of the data conclusively produced dynamic exponents of the glass transition z~9 considerably higher than theoretically predicted and previously reported. In high-dissipative measurements a voltage instability appearing in the current-voltage characteristics of type II superconductors was observed for the first time in BSCCO and shown to result from a Larkin-Ovchinnikov flux-flow vortex instability under the influence of quasi-particle heating. However, in an analogous investigation of YBCO the instability was found to appear only in the temperature and magnetic-field regime of the vortex-glass state. Rapid-pulse measurements fully confirmed this correlation of vortex glass and instability in YBCO and revealed a constant rise time (~µs).

Vortex dynamics in superconductors in the presence of anisotropic pinning

Vortex dynamics in two different classes of superconductors with anisotropic unidirected pinning sites was experimentally investigated by magnetoresistivity measurements: YBCO−films with unidirected twins and Nb-films deposited on faceted $mathrm Al_2O_3$ substrate surfaces. For the interpretation of the experimental results a theoretical model based on the Fokker-Planck equation was used. It was proved by X-ray measurements that YBCO films prepared on (001) $mathrm NdGaO_3$ substrates exhibit only one twin orientation in contrast to YBCO films grown on (100) $mathrm SrTiO_$3 substrates. The magnetoresistivity measurements of the YBCO films with unidirected twin boundaries revealed the existence of two new magnetoresistivity components, which is a characteristic feature of a guided vortex motion: an odd longitudinal component with respect to the magnetic field sign reversal and an even transversal component. However, due to the small coherence length in YBCO and the higher density of point-like defects comparing to high-quality YBCO single crystals, the strength of the isotropic point pinning was comparable with the strength of the pinning produced by twins. This smeared out all effects caused by the pinning anisotropy. The behaviour of the odd longitudinal component was found to be independent of the transport current direction with respect to the twin planes. The magnetoresistivity measurements of faceted Nb films demonstrated the appearance of an odd longitudinal and even transversal component of the magnetoresistivity. The temperature and magnetic field dependences of all relevant magnetoresistivity components were measured. The angles between the average vortex velocity vector and the transport current direction calculated from the experimental data for the different transport current orientations with respect to the facet ridges showed that the vortices moved indeed along the facet ridges. An anomalous Hall effect, i.e. a sign change of the odd transversal magnetoresistivity, has been found in the temperature and magnetic field dependences of the Hall resisitivity of the samples. The theory developed by V.~A.~Shklovskij was used for the explanation of the experimental data. It shows very good agreement with the experiment. The temperature dependence of the even longitudinal magnetoresistivity component of the samples could be very well fitted within the theoretical approach, using for the isotropic and anisotropic pinning potential simple potential with a symmetric triangular potential wells whose depths were estimated from the experimental data.

O (alpha 4 s) loop-by-loop contributions to heavy quark pair production in hadronic collisions

The present state of the theoretical predictions for the hadronic heavy hadron production is not quite satisfactory. The full next-to-leading order (NLO) ${cal O} (alpha_s^3)$ corrections to the hadroproduction of heavy quarks have raised the leading order (LO) ${cal O} (alpha_s^2)$ estimates but the NLO predictions are still slightly below the experimental numbers. Moreover, the theoretical NLO predictions suffer from the usual large uncertainty resulting from the freedom in the choice of renormalization and factorization scales of perturbative QCD.In this light there are hopes that a next-to-next-to-leading order (NNLO) ${cal O} (alpha_s^4)$ calculation will bring theoretical predictions even closer to the experimental data. Also, the dependence on the factorization and renormalization scales of the physical process is expected to be greatly reduced at NNLO. This would reduce the theoretical uncertainty and therefore make the comparison between theory and experiment much more significant. In this thesis I have concentrated on that part of NNLO corrections for hadronic heavy quark production where one-loop integrals contribute in the form of a loop-by-loop product. In the first part of the thesis I use dimensional regularization to calculate the ${cal O}(ep^2)$ expansion of scalar one-loop one-, two-, three- and four-point integrals. The Laurent series of the scalar integrals is needed as an input for the calculation of the one-loop matrix elements for the loop-by-loop contributions. Since each factor of the loop-by-loop product has negative powers of the dimensional regularization parameter $ep$ up to ${cal O}(ep^{-2})$, the Laurent series of the scalar integrals has to be calculated up to ${cal O}(ep^2)$. The negative powers of $ep$ are a consequence of ultraviolet and infrared/collinear (or mass ) divergences. Among the scalar integrals the four-point integrals are the most complicated. The ${cal O}(ep^2)$ expansion of the three- and four-point integrals contains in general classical polylogarithms up to ${rm Li}_4$ and $L$-functions related to multiple polylogarithms of maximal weight and depth four. All results for the scalar integrals are also available in electronic form. In the second part of the thesis I discuss the properties of the classical polylogarithms. I present the algorithms which allow one to reduce the number of the polylogarithms in an expression. I derive identities for the $L$-functions which have been intensively used in order to reduce the length of the final results for the scalar integrals. I also discuss the properties of multiple polylogarithms. I derive identities to express the $L$-functions in terms of multiple polylogarithms. In the third part I investigate the numerical efficiency of the results for the scalar integrals. The dependence of the evaluation time on the relative error is discussed. In the forth part of the thesis I present the larger part of the ${cal O}(ep^2)$ results on one-loop matrix elements in heavy flavor hadroproduction containing the full spin information. The ${cal O}(ep^2)$ terms arise as a combination of the ${cal O}(ep^2)$ results for the scalar integrals, the spin algebra and the Passarino-Veltman decomposition. The one-loop matrix elements will be needed as input in the determination of the loop-by-loop part of NNLO for the hadronic heavy flavor production.

Top-quark pair production at hadron colliders

In this thesis we investigate several phenomenologically important properties of top-quark pair production at hadron colliders. We calculate double differential cross sections in two different kinematical setups, pair invariant-mass (PIM) and single-particle inclusive (1PI) kinematics. In pair invariant-mass kinematics we are able to present results for the double differential cross section with respect to the invariant mass of the top-quark pair and the top-quark scattering angle. Working in the threshold region, where the pair invariant mass M is close to the partonic center-of-mass energy sqrt{hat{s}}, we are able to factorize the partonic cross section into different energy regions. We use renormalization-group (RG) methods to resum large threshold logarithms to next-to-next-to-leading-logarithmic (NNLL) accuracy. On a technical level this is done using effective field theories, such as heavy-quark effective theory (HQET) and soft-collinear effective theory (SCET). The same techniques are applied when working in 1PI kinematics, leading to a calculation of the double differential cross section with respect to transverse-momentum pT and the rapidity of the top quark. We restrict the phase-space such that only soft emission of gluons is possible, and perform a NNLL resummation of threshold logarithms. The obtained analytical expressions enable us to precisely predict several observables, and a substantial part of this thesis is devoted to their detailed phenomenological analysis. Matching our results in the threshold regions to the exact ones at next-to-leading order (NLO) in fixed-order perturbation theory, allows us to make predictions at NLO+NNLL order in RG-improved, and at approximate next-to-next-to-leading order (NNLO) in fixed order perturbation theory. We give numerical results for the invariant mass distribution of the top-quark pair, and for the top-quark transverse-momentum and rapidity spectrum. We predict the total cross section, separately for both kinematics. Using these results, we analyze subleading contributions to the total cross section in 1PI and PIM originating from power corrections to the leading terms in the threshold expansions, and compare them to previous approaches. We later combine our PIM and 1PI results for the total cross section, this way eliminating uncertainties due to these corrections. The combined predictions for the total cross section are presented as a function of the top-quark mass in the pole, the minimal-subtraction (MS), and the 1S mass scheme. In addition, we calculate the forward-backward (FB) asymmetry at the Tevatron in the laboratory, and in the ttbar rest frames as a function of the rapidity and the invariant mass of the top-quark pair at NLO+NNLL. We also give binned results for the asymmetry as a function of the invariant mass and the rapidity difference of the ttbar pair, and compare those to recent measurements. As a last application we calculate the charge asymmetry at the LHC as a function of a lower rapidity cut-off for the top and anti-top quarks.