The effect of changes in the bulk dielectric constant on the DNA torsional properties

The effect of changes in the bulk dielectric constant on the DNA torsional properties was evaluated from plasmid circularization reactions. In these reactions, pUC18 previously linearized by EcoRI digestion was recircularized with T4 DNA ligase. The bulk dielectric constant of the reaction medium was decreased by the addition of different concentrations of neutral solutes: ethylene glycol, glycerol, sorbitol, and sucrose, or increased by the addition of glycine. The topoisomers generated by the ligase reaction were resolved by agarose-gel electrophoresis. The DNA twist energy parameter (K), which is an apparent torsional constant, was determined by linearization of the Gaussian topoisomers' distribution. It was observed that the twist energy parameter for the given solutes is almost linearly dependent on the bulk dielectric constant. In the reaction buffer, the twist energy parameter was determined to be 1100 +/- 100. By decreasing the dielectric constant to 74 with the addition of sorbitol, the value of the parameter reaches K = 900 +/- 100, whereas the addition of ethylene glycol leads to kappa = 400 +/- 50. Upon addition of glycine, which resulted in a dielectric constant equal to 91, the value of the twist energy parameter increased to K 1750 +/- 100. (c) 2007 Wiley Periodicals.

Uso de modelo de rede no estudo do enovelamento de proteínas

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Prediction of nonlocal scaling parameter for armchair and zigzag single-walled carbon nanotubes based on molecular structural mechanics, nonlocal elasticity and wave propagation

Atomic vibration in the Carbon Nanotubes (CNTs) gives rise to non-local interactions. In this paper, an expression for the non-local scaling parameter is derived as a function of the geometric and electronic properties of the rolled graphene sheet in single-walled CNTs. A self-consistent method is developed for the linearization of the problem of ultrasonic wave propagation in CNTs. We show that (i) the general three-dimensional elastic problem leads to a single non-local scaling parameter (e(0)), (ii) e(0) is almost constant irrespective of chirality of CNT in the case of longitudinal wave propagation, (iii) e(0) is a linear function of diameter of CNT for the case of torsional mode of wave propagation, (iv) e(0) in the case of coupled longitudinal-torsional modes of wave propagation, is a function which exponentially converges to that of axial mode at large diameters and to torsional mode at smaller diameters. These results are valid in the long-wavelength limit. (C) 2011 Elsevier Ltd. All rights reserved.

Design and Evaluation of Torsional Probes for Multifrequency Atomic Force Microscopy

Multifrequency atomic force microscopy is a powerful nanoscale imaging and characterization technique that involves excitation of the atomic force microscope (AFM) probe and measurement of its response at multiple frequencies. This paper reports the design, fabrication, and evaluation of AFM probes with a specified set of torsional eigen-frequencies that facilitate enhancement of sensitivity in multifrequency AFM. A general approach is proposed to design the probes, which includes the design of their generic geometry, adoption of a simple lumped-parameter model, guidelines for determination of the initial dimensions, and an iterative scheme to obtain a probe with the specified eigen-frequencies. The proposed approach is employed to design a harmonic probe wherein the second and the third eigen-frequencies are the corresponding harmonics of the first eigen-frequency. The probe is subsequently fabricated and evaluated. The experimentally evaluated eigen-frequencies and associated mode shapes are shown to closely match the theoretical results. Finally, a simulation study is performed to demonstrate significant improvements in sensitivity to the second-and the third-harmonic spectral components of the tip-sample interaction force with the harmonic probe compared to that of a conventional probe.

Solar photospheric and coronal abundances from solar energetic particle measurements

Observations of solar energetic particles (SEPs) from 22 solar flares in the 1977-1982 time period are reported. The observations were made by the Cosmic Ray Subsystem on board the Voyager 1 and 2 spacecraft. SEP abundances have been obtained for all elements with 3 ≤ Z ≤ 30 except Li, Be, B. F, Sc, V, Co and Cu. for which upper limits have been obtained. Statistically meaningful abundances of several rare elements (e.g., P, Cl, K, Ti, Mn) have been determined for the first time, and the average abundances of the more abundant elements have been determined with improved precision, typically a factor of three better than the best previous determinations.

Previously reported results concerning the dependence of the fractionation of SEPs relative to photosphere on first ionization potential (FIP) have been confirmed and amplified upon with the new data. The monotonic Z-dependence of the variation between flares noted by earlier studies was found to be interpretable as a fractionation, produced by acceleration of the particles from the corona and their propagation through interplanetary space, which is ordered by the ionic charge-to-mass ratio Q/ M of the species making up the SEPs. It was found that Q/M is the primary organizing parameter of acceleration and propagation effects in SEPs, as evidenced by the dependence on Q/M of time, spatial and energy dependence within flares and of the abundance variability from flare to flare.

An unfractionated coronal composition was derived by applying a simple Q/M fractionation correction to the observed average SEP composition, to simultaneously correct for all Q/M-correlated acceleration/propagation fractionation of SEPs. The resulting coronal composition agrees well with current XUV/X-ray spectroscopic measurements of coronal composition but is of much higher precision and is available for a much larger set of elements. Compared to spectroscopic photospheric abundances, the SEP-derived corona appears depleted in C and somewhat enriched in Cr (and possibly Ca and Ti).

An unfractionated photospheric composition was derived by applying a simple FIP fractionation correction to the derived coronal composition, to correct for the FIP-associated fractionation of the corona during its formation from photospheric material. The resulting composition agrees well with the photospheric abundance tabulation of Grevesse (1984) except for an at least 50% lower abundance of C and a significantly greater abundance of Cr and possibly Ti. The results support the Grevesse photospheric Fe abundance, about 50% higher than meteoritic and earlier solar values. The SEP-derived photospheric composition is not generally of higher precision than the available spectroscopic data, but it relies on fewer physical parameters and is available for some elements (C, N, Ne, Ar) which cannot be measured spectroscopically in the photosphere.

Transmission matrices and lumped parameter models for continuous systems

The use of transmission matrices and lumped parameter models for describing continuous systems is the subject of this study. Non-uniform continuous systems which play important roles in practical vibration problems, e.g., torsional oscillations in bars, transverse bending vibrations of beams, etc., are of primary importance.

A new approach for deriving closed form transmission matrices is applied to several classes of non-uniform continuous segments of one dimensional and beam systems. A power series expansion method is presented for determining approximate transmission matrices of any order for segments of non-uniform systems whose solutions cannot be found in closed form. This direct series method is shown to give results comparable to those of the improved lumped parameter models for one dimensional systems.

Four types of lumped parameter models are evaluated on the basis of the uniform continuous one dimensional system by comparing the behavior of the frequency root errors. The lumped parameter models which are based upon a close fit to the low frequency approximation of the exact transmission matrix, at the segment level, are shown to be superior. On this basis an improved lumped parameter model is recommended for approximating non-uniform segments. This new model is compared to a uniform segment approximation and error curves are presented for systems whose areas very quadratically and linearly. The effect of varying segment lengths is investigated for one dimensional systems and results indicate very little improvement in comparison to the use of equal length segments. For purposes of completeness, a brief summary of various lumped parameter models and other techniques which have previously been used to approximate the uniform Bernoulli-Euler beam is a given.

Flexibility and torsional resistance of three nickel-titanium retreatment instrument systems

Aim To assess the dimensional characteristics, flexibility and torsional behaviour of nickel-titanium retreatment instruments. Methodology Using image analysis software and high-resolution digital images, the instrument length, tip angle, diameter at 3mm from the tip and the distance between the blades (pitch length) of the following eight instruments were measured (n=12 for each measurement parameter): the ProTaper Universal retreatment (PTU-R) D1, D2 and D3 instruments; the R-Endo R1, R2 and R3 retreatment instruments; and the Mtwo retreatment (Mtwo-R) sizes 25 and 15 retreatment instruments. Maximum torque and the angular deflection at fracture as well as the bending moment at 45° were measured (n=12) according to the International Standards Organisation (ISO) specification number 3630-1. Data were analysed using the analysis of variance (α=0.05). Results The length of the active part of the instruments was found to vary according to the depth of the canal into which they were designed to reach. The pitch length also increased along the active length. The PTU-R D1 and the Mtwo-R instruments had active tips. Measurements of the bending moment at 45° revealed that the Mtwo-R 15 instrument was the most flexible, whereas the PTU-R D1 was the least flexible. The maximum torque tended to increase as the instrument diameter at 3mm from the tip increased, whereas the angular deflection at fracture varied in the opposite direction. Conclusions The geometrical characteristics of the retreatment instruments and their flexibility and torsion behaviour were consistent with their intended clinical application. © 2011 International Endodontic Journal.

Realisierung der IceCube MonteCarlo-Produktion im WLCG und Untersuchung von Auswirkungen meteorologischer Parameter auf die Erzeugung atmosphärischer Myonen

Das am Südpol gelegene Neutrinoteleskop IceCube detektiert hochenergetische Neutrinos über die schwache Wechselwirkung geladener und neutraler Ströme. Die Analyse basiert auf einem Vergleich mit Monte-Carlo-Simulationen, deren Produktion global koordiniert wird. In Mainz ist es erstmalig gelungen, Simulationen innerhalb der Architektur des Worldwide LHC Computing Grid (WLCG) zu realisieren, was die Möglichkeit eröffnet, Monte-Carlo-Berechnungen auch auf andere deutsche Rechnerfarmen (CEs) mit IceCube-Berechtigung zu verteilen. Atmosphärische Myonen werden mit einer Rate von über 1000 Ereignissen pro Sekunde aufgezeichnet. Eine korrekte Interpretation dieses dominanten Signals, welches um einen Faktor von 10^6 reduziert werden muss um das eigentliche Neutrinosignal zu extrahieren, ist deswegen von großer Bedeutung. Eigene Simulationen mit der Software-Umgebung CORSIKA wurden durchgeführt um die von Energie und Einfallswinkel abhängige Entstehungshöhe atmosphärischer Myonen zu bestimmen. IceCube Myonraten wurden mit Wetterdaten des European Centre for Medium-Range Weather Forcasts (ECMWF) verglichen und Korrelationen zwischen jahreszeitlichen sowie kurzzeitigen Schwankungen der Atmosphärentemperatur und Myonraten konnten nachgewiesen werden. Zudem wurde eine Suche nach periodischen Effekten in der Atmosphäre, verursacht durch z.B. meteorologische Schwerewellen, mit Hilfe einer Fourieranalyse anhand der IceCube-Daten durchgeführt. Bislang konnte kein signifikanter Nachweis zur Existenz von Schwerewellen am Südpol erbracht werden.

Search for Dark Matter in events with a highly energetic jet and missing transverse momentum in proton-proton collisions at root out s = 8 TeV with the ATLAS detector

The experiments at the Large Hadron Collider at the European Centre for Particle Physics, CERN, rely on efficient and reliable trigger systems for singling out interesting events. This thesis documents two online timing monitoring tools for the central trigger of the ATLAS experiment as well as the adaption of the central trigger simulation as part of the upgrade for the second LHC run. Moreover, a search for candidates for so-called Dark Matter, for which there is ample cosmological evidence, is presented. This search for generic weakly interacting massive particles (WIMPs) is based on the roughly 20/fb of proton-proton collisions at a centre-of-mass-energy of sqrt{s}=8 TeV recorded with the ATLAS detector in 2012. The considered signature are events with a highly energetic jet and large missing transverse energy. No significant deviation from the theory prediction is observed. Exclusion limits are derived on parameters of different signal models and compared to the results of other experiments. Finally, the results of a simulation study on the potential of the analysis at sqrt{s}=14 TeV are presented.

An accurate model for simulating energetic behavior of PV grid connected inverters

This paper proposes a new model for characterizing the energetic behavior of grid connected PV inverters. The model has been obtained from a detailed study of main loss processes in small size PV inverters in the market. The main advantage of the used method is to obtain a model that comprises two antagonistic features, since both are simple, easy to compute and apply, and accurate. One of the main features of this model is how it handles the maximum power point tracking (MPPT) and the efficiency: in both parts the model uses the same approach and it is achieved by two resistive elements which simulate the losses inherent to each parameter. This makes this model easy to implement, compact and refined. The model presented here also includes other parameters, such as start threshold, standby consumption and islanding behavior. In order to validate the model, the values of all the parameters listed above have been obtained and adjusted using field measurements for several commercial inverters, and the behavior of the model applied to a particular inverter has been compared with real data under different working conditions, taken from a facility located in Madrid. The results show a good fit between the model values and the real data. As an example, the model has been implemented in PSPICE electronic simulator, and this approach has been used to teach grid-connected PV systems. The use of this model for the maintenance of working PV facilities is also shown.

On arterial contractility, energetic requirements of the cardiovascular system, and the formation of arterial sclerosis

The aorta has been viewed as a passive distribution manifold for blood whose elasticity allows it to store blood during cardiac ejection (systole), and release it during relaxation (diastole). This capacitance, or compliance, lowers peak cardiac work input and maintains peripheral sanguine irrigation throughout the cardiac cycle. The compliance of the human and canine circulatory systems have been described either as constant throughout the cycle (Toy et al. 1985) or as some inverse function of pressure (Li et al. 1990, Cappelo et al. 1995). This work shows that a compliance value that is higher during systole than diastole (equivalent to a direct function of pressure) leads to a reduction in the energetic input to the cardiovascular system (CV), even when accounting for the energy required to change compliance. This conclusion is obtained numerically, based on a 3-element lumped-parameter model of the CV, then demonstrated in a physical model built for the purpose. It is then shown, based on the numerical and physical models, on analytical considerations of elastic tubes, and on the analysis of arterial volume as a function of pressure measured in vivo (Armentano et al. 1995), that the mechanical effects of a presupposed arterial contraction are consistent with those of energetically beneficial changes in compliance during the cardiac cycle. Although the amount of energy potentially saved with rhythmically contracting arteries is small (mean 0.55% for the cases studied) the importance of the phenomenon lies in its possible relation to another function of the arterial smooth muscle (ASM): synthesis of wall matrix macromolecules. It is speculated that a reduction in the rate of collagen synthesis by the ASM is implicated in the formation of arteriosclerosis. ^