Estimates of electronic coupling for excess electron transfer in DNA

Electronic coupling Vda is one of the key parameters that determine the rate of charge transfer through DNA. While there have been several computational studies of Vda for hole transfer, estimates of electronic couplings for excess electron transfer (ET) in DNA remain unavailable. In the paper, an efficient strategy is established for calculating the ET matrix elements between base pairs in a π stack. Two approaches are considered. First, we employ the diabatic-state (DS) method in which donor and acceptor are represented with radical anions of the canonical base pairs adenine-thymine (AT) and guanine-cytosine (GC). In this approach, similar values of Vda are obtained with the standard 6-31 G* and extended 6-31++ G* basis sets. Second, the electronic couplings are derived from lowest unoccupied molecular orbitals (LUMOs) of neutral systems by using the generalized Mulliken-Hush or fragment charge methods. Because the radical-anion states of AT and GC are well reproduced by LUMOs of the neutral base pairs calculated without diffuse functions, the estimated values of Vda are in good agreement with the couplings obtained for radical-anion states using the DS method. However, when the calculation of a neutral stack is carried out with diffuse functions, LUMOs of the system exhibit the dipole-bound character and cannot be used for estimating electronic couplings. Our calculations suggest that the ET matrix elements Vda for models containing intrastrand thymine and cytosine bases are essentially larger than the couplings in complexes with interstrand pyrimidine bases. The matrix elements for excess electron transfer are found to be considerably smaller than the corresponding values for hole transfer and to be very responsive to structural changes in a DNA stack

Anharmonic force constant calculations

The relationship of the anharmonic force constants in curvilinear internal coordinates to the observed vibration-rotation spectrum of a molecule is reviewed. A simplified method of setting up the required non-linear coordinate transformations is described: this makes use of an / tensor, which is a straightforward generalization of the / matrix used in the customary description of harmonic force constant calculations. General formulae for the / tensor elements, in terms of the familiar L matrix elements, are presented. The use of non-linear symmetry coordinates and redundancies are described. Sample calculations on the water and ammonia molecules are reported.

Coriolis interactions about x-y axes in symmetric tops

Selection rules and matrix elements are derived for Coriolis interactions between vibrational levels due to rotation about (x, y) axes in symmetric top molecules. The theory is developed in detail for the case of interaction between an A1 and an E species vibrational level in a C3v molecule; perturbations to both the positions and the intensities of the rovibration transitions in the spectrum are considered. A computer program has been written which calculates exactly the perturbed spectrum of two interacting rovibration bands according to this model, the results being presented directly by a graph plotter connected to the computer. This has been used to interpret perturbations observed in two pairs of interacting fundamentals in the spectrum of CH3F (ν2 - ν5 and ν3 - ν6) and one pair in CD3Cl (ν2 - ν5). The resulting analysis of the observed spectrum leads to new values for some vibration-rotation interaction constants and also leads to a unique determination of the sign relationship between the dipole moment derivatives in each pair of interacting normal vibrations. These sign relations are summarized in Figs. 8, 12, and 15.

The calculation of accurate normal coordinates I: general theory, and application to methane

The calculation of accurate and reliable vibrational potential functions and normal co-ordinates is discussed, for such simple polyatomic molecules as it may be possible. Such calculations should be corrected for the effects of anharmonicity and of resonance interactions between the vibrational states, and should be fitted to all the available information on all isotopic species: particularly the vibrational frequencies, Coriolis zeta constants and centrifugal distortion constants. The difficulties of making these corrections, and of making use of the observed data are reviewed. A programme for the Ferranti Mercury Computer is described by means of which harmonic vibration frequencies and normal co-ordinate vectors, zeta factors and centrifugal distortion constants can be calculated, from a given force field and from given G-matrix elements, etc. The programme has been used on up to 5 × 5 secular equations for which a single calculation and output of results takes approximately l min; it can readily be extended to larger determinants. The best methods of using such a programme and the possibility of reversing the direction of calculation are discussed. The methods are applied to calculating the best possible vibrational potential function for the methane molecule, making use of all the observed data.

Variational calculations of rovibrational states: a precise high-energy potential surface for HCN [and discussion]

We report the results of variational calculations of the rovibrational energy levels of HCN for J = 0, 1 and 2, where we reproduce all the ca. 100 observed vibrational states for all observed isotopic species, with energies up to 18000 cm$^{-1}$, to about $\pm $1 cm$^{-1}$, and the corresponding rotational constants to about $\pm $0.001 cm$^{-1}$. We use a hamiltonian expressed in internal coordinates r$_{1}$, r$_{2}$ and $\theta $, using the exact expression for the kinetic energy operator T obtained by direct transformation from the cartesian representation. The potential energy V is expressed as a polynomial expansion in the Morse coordinates y$_{i}$ for the bond stretches and the interbond angle $\theta $. The basis functions are built as products of appropriately scaled Morse functions in the bond-stretches and Legendre or associated Legendre polynomials of cos $\theta $ in the angle bend, and we evaluate matrix elements by Gauss quadrature. The hamiltonian matripx is factorized using the full rovibrational symmetry, and the basis is contracted to an optimized form; the dimensions of the final hamiltonian matrix vary from 240 $\times $ 240 to 1000 $\times $ 1000.We believe that our calculation is converged to better than 1 cm$^{-1}$ at 18 000 cm$^{-1}$. Our potential surface is expressed in terms of 31 parameters, about half of which have been refined by least squares to optimize the fit to the experimental data. The advantages and disadvantages and the future potential of calculations of this type are discussed.

Rovibrational energy levels of hydrogen peroxide, studied by MULTIMODE with a reaction path Hamiltonian

Recently. Carter and Handy [J. Chem. Phys. 113 (2000) 987] have introduced the theory of the reaction path Hamiltonian (RPH) [J. Chem. Phys. 72 (1980) 99] into the variational scheme MULTIMODE, for the calculation of the J = 0 vibrational levels of polyatomic molecules, which have a single large-amplitude motion. In this theory the reaction path coordinate s becomes the fourth dimension of the moment-of-inertia tensor, and must be treated separately from the remaining 3N - 7 normal coordinates in the MULTIMODE program. In the modified program, complete integration is performed over s, and the M-mode MULTIMODE coupling approximation for the evaluation of the matrix elements applies only to the 3N - 7 normal coordinates. In this paper the new algorithm is extended to the calculation of rotational-vibration energy levels (i.e. J > 0) with the RPH, following from our analogous implementation for rigid molecules [Theoret. Chem. Acc. 100 (1998) 191]. The full theory is given, and all extra terms have been included to give the exact kinetic energy operator. In order to validate the new code, we report studies on hydrogen peroxide (H2O2), where the reaction path is equivalent to torsional motion. H2O2 has previously been studied variationally using a valence coordinate Hamiltonian; complete agreement for calculated rovibrational levels is obtained between the previous results and those from the new code, using the identical potential surface. MULTIMODE is now able to calculate rovibrational levels for polyatomic molecules which have one large-amplitude motion. (C) 2003 Elsevier B.V. All rights reserved.

Theoretical rovibrational line intensities in the electronic ground state of ozone

First-principles calculations of absolute line intensities and rovibrational energies of ozone (O-16(3)) are reported using potential energy and electric dipole moment functions calculated by the internally contracted MRCI approach. The rovibrational energies and eigenfunctions (up to about 8500 cm(-1) and J = 64) were obtained variationally with an exact Hamiltonian in internal valence coordinates. More than 4.8 x 10(6) electric dipole transition matrix elements were calculated for the absolute rovibrational line intensities. They are compared with the values of the HITRAN database. The purely rotational absolute line intensities in the (000) state and the rovibrational intensities for the (001)-(000) band agree to within about 0.3 to 1% for the (0 10)-(000) band to within about 3 to 4%. Excellent agreement with experiment is also achieved for low-lying overtone and combination bands. Inconsistencies are found for the (100)-(000) band overlapping with the antisymmetric stretching fundamental and also for the (002)-(000) antisymmetric stretching overtone. The generated dipole moment function can be used for predicting the absorption intensities in any of the heavier isotopomers, hot bands or the rates of spontaneous emission.

Rapid selective separation of americium/curium from simulated nuclear forensic matrices using triazine ligands

In analysis of complex nuclear forensic samples containing lanthanides, actinides and matrix elements, rapid selective extraction of Am/Cm for quantification is challenging, in particular due the difficult separation of Am/Cm from lanthanides. Here we present a separation process for Am/Cm(III) which is achieved using a combination of AG1-X8 chromatography followed by Am/Cm extraction with a triazine ligand. The ligands tested in our process were CyMe4-BTPhen, CyMe4- BTBP, CA-BTP and CA-BTPhen. Our process allows for purification and quantification of Am and Cm (recoveries 80%–100%) and other major actinides in < 2d without the use of multiple columns or thiocyanate. The process is unaffected by high level Ca(II)/Fe(III)/Al(III) (10mg mL−1) and thus requires little pre-treatment of samples.

WRITING ELECTRONIC FERROMAGNETIC STATES IN A HIGH-TEMPERATURE PARAMAGNETIC NUCLEAR SPIN SYSTEM

In this paper, we use Nuclear Magnetic Resonance (NMR) to write electronic states of a ferromagnetic system into high-temperature paramagnetic nuclear spins. Through the control of phase and duration of radio frequency pulses, we set the NMR density matrix populations, and apply the technique of quantum state tomography to experimentally obtain the matrix elements of the system, from which we calculate the temperature dependence of magnetization for different magnetic fields. The effects of the variation of temperature and magnetic field over the populations can be mapped in the angles of spin rotations, carried out by the RF pulses. The experimental results are compared to the Brillouin functions of ferromagnetic ordered systems in the mean field approximation for two cases: the mean field is given by (i) B = B(0) + lambda M and (ii) B = B(0) + lambda M + lambda`M(3), where B(0) is the external magnetic field, and lambda, lambda` are mean field parameters. The first case exhibits second order transition, whereas the second case has first order transition with temperature hysteresis. The NMR simulations are in good agreement with the magnetic predictions.

A study of the relaxation dynamics in a quadrupolar NMR system using Quantum State Tomography

This article reports a relaxation study in an oriented system containing spin 3/2 nuclei using quantum state tomography (QST). The use of QST allowed evaluating the time evolution of all density matrix elements starting from several initial states. Using an appropriated treatment based on the Redfield theory, the relaxation rate of each density matrix element was measured and the reduced spectral densities that describe the system relaxation were determined. All the experimental data could be well described assuming pure quadrupolar relaxation and reduced spectral densities corresponding to a superposition of slow and fast motions. The data were also analyzed in the context of Quantum Information Processing, where the coherence loss of each qubit of the system was determined using the partial trace operation. (C) 2008 Elsevier Inc. All rights reserved.

Fazer a ponte para a escola de todos(as)

The purpose of this study is to understand what are the matrix elements in which everyday activities of social author/authors, actor/actors and actress/actresses are embedded, in order to carry out the Escola da Ponte s political and pedagogic process (PPP). Thus, the object of this study is to reflect on an experience developed in a public school supported by the Portuguese State within the scenario of institutions that are committed to building up a school of the people by investing in democratization and community participation in their management process. The methodological course of action was targeted at the presuppositions of qualitative research (WOODS, 1999; BURGESS, 1997; MILLS, 1982; OLIVEIRA, 1998; BOGDAN and BIKLEN, 1994; MACEDO, 2000; CASAL, 1996; GEERTZ, 2000), with data collected from random word association (MACHADO and CARVALHO, 2003), the discourse of the interviewed (KAUFMANN, 1996; SILVA, 2006; 2002), observation notes and documents (ELIAS, 1997). Based on a multiple reference and theoretical framework, the investigation revealed elements that are construed as the raw material and pillars supporting the bridge of a school of the people, as well as the self-organization of the school community which emerges as a dimension that binds together all the elements and brings new arrangements into the school dynamics by moving from the individual to the society (DUPUY, 1990). Along this line, the central argument is that in the short and long run the public school quality does not spring from macro educational policies, nor from ephemeral mass-production programs, projects or governmental policies, but from the intent of the professionals working there in becoming authors and characters in the process of building up and carrying out the PPP. The Project has been conceived in the light of the needs and intentionality of the community whose support comes from the participation and social control held by the students families and the community s power to force to action public administration central agencies aiming at having the State fulfill its responsibilities

Single real transformation matrices applied to double three-phase transmission lines

Single real transformation matrices are tested as phase-mode transformation matrices of typical symmetrical systems with double three-phase and two parallel double three-phase transmission lines. These single real transformation matrices are achieved from eigenvector matrices of the mentioned systems and they are based on Clarke's matrix. Using linear combinations of the Clarke's matrix elements, the techniques applied to the single three-phase lines are extended to systems with 6 or 12 phase conductors. For transposed double three-phase lines, phase Z and Y matrices are changed into diagonal matrices in mode domain. Considering non-transposed cases of double three-phase lines, the results are not exact and the error analyses are performed using the exact eigenvalues. In case of two parallel double three-phase lines, the exact single real transformation matrix has not been obtained yet. Searching for this exact matrix, the analyses are based on a single homopolar reference. For all analyses in this paper, the homopolar mode is used as the only homopolar reference for all phase conductors of the studied system. (C) 2008 Elsevier B.V. All rights reserved.

Oestrogen supplementation following castration promotes stromal remodelling and histopathological alterations in the Mongolian gerbil ventral prostate

The effect of oestradiol on the intact and castrated adult gerbil prostate was evaluated by focussing on stromal and epithelial disorders, and hormonal receptor immunoreactivity. The experimental animals were studied by histological, histochemical and immunohistochemical techniques, morphometric-stereological analysis and transmission electron microscopy. Epithelial alterations in the oestradiol-treated animals were frequent, with an increase in epithelial cell height, areas of intense dysplasia and hyperplasia and formation of prostatic intraepithelial neoplasia (PIN). Another aspect that did not depend on the presence of testosterone was the arrangement of the fibrillar and non-fibrillar elements of the extracellular matrix among smooth muscle cells (SMC), suggesting a possible role of these cells in rearrangement and synthesis of these components, after oestrogenic treatment. In the castrated animals, an accumulation of extracellular matrix elements under the epithelium was evident, while in the intact animals the same compounds were dispersed and scarce. In the groups of intact and castrated animals, SMC and fibroblasts exhibited a secretory phenotype, which was accentuated after oestradiol administration. There was an increase of the immunoreactivity to alpha-oestrogen and androgen receptors in hyperplastic areas compared to normal epithelium, revealing the involvement of these steroid receptors in the hyperplasia and PIN development.

Integrable aspects of the scaling q-state Potts models I: bound states and bootstrap closure

We discuss the q-state Potts models for q less than or equal to 4, in the scaling regimes close to their critical or tricritical points. Starting from the kink S-matrix elements proposed by Chim and Zamolodchikov, the bootstrap is closed for the scaling regions of all critical points, and for the tricritical points when 4 > q greater than or equal to 2. We also note a curious appearance of the extended last line of Freudenthal's magic square in connection with the Potts models. (C) 2003 Elsevier B.V. B.V. All rights reserved.

Trilepton signal for supersymmetry at the Fermilab Tevatron reexamined

Within a wide class of models, the CERN LEP2 lower limit of 95 GeV on the chargino mass implies gluinos are heavier than similar to 300 GeV. In this case electroweak (W) over tilde(1)(W) over tilde(1) production and (W) over tilde(1)(Z) over tilde(2) production are the dominant supersymmerry (SUSY) processes at the Fermilab Tevatron, and the extensively examined isolated trilepton signal From (W) over tilde(1)(Z) over tilde(2) production assumes an even greater importance. We update our previous calculations of the SUSY reach of luminosity upgrades of the Fermilab Tevatron in this channel incorporating (i) decay matrix elements in the computation of the momenta of leptons from chargino and neutralino decays, (ii) the trilepton background from W*Z* and W*gamma* production which, though neglected in previous analyses, turns out to be the dominant background, and finally, (iii) modified sets of cuts designed to reduce these new backgrounds and increase the range of model parameters for which the signal is observable. We show our improved projections for the reach for SUSY of both the Fermilab Main Injector and the proposed TeV33 upgrade. We also present opposite sign same flavor dilepton invariant mass distributions as well as the p(T) distributions of leptons in SUSY trilepton events, and comment upon how the inclusion of decay matrix elements impacts upon the Tevatron reach, as well as upon the extraction of neutralino masses.