Chaotic transport in reversed shear tokamaks

For tokamak models using simplified geometries and reversed shear plasma profiles, we have numerically investigated how the onset of Lagrangian chaos at the plasma edge may affect the plasma confinement in two distinct but closely related problems. Firstly, we have considered the motion of particles in drift waves in the presence of an equilibrium radial electric field with shear. We have shown that the radial particle transport caused by this motion is selective in phase space, being determined by the resonant drift waves and depending on the parameters of both the resonant waves and the electric field profile. Moreover, we have shown that an additional transport barrier may be created at the plasma edge by increasing the electric field. In the second place, we have studied escape patterns and magnetic footprints of chaotic magnetic field lines in the region near a tokamak wall, when there are resonant modes due to the action of an ergodic magnetic limiter. A non-monotonic safety factor profile has been used in the analysis of field line topology in a region of negative magnetic shear. We have observed that, if internal modes are perturbed, the distributions of field line connection lengths and magnetic footprints exhibit spatially localized escape channels. For typical physical parameters of a fusion plasma, the two Lagrangian chaotic processes considered in this work can be effective in usual conditions so as to influence plasma confinement. The reversed shear effects discussed in this work may also contribute to evaluate the transport barrier relevance in advanced confinement scenarios in future tokamak experiments.

Electronic spectroscopy of biomolecules in solution: fluorescein dianion in water

A combined and sequential Monte Carlo-quantum mechanics methodology is used to describe the electronic absorption spectrum of the fluorescein dianion in water. Different sets of 100 statistically relevant configurations composed of the solute and several solvent molecules are sampled from the Monte Carlo simulation for a posteriori quantum mechanical calculations of the spectra. In the largest case the configurations are composed of fluorescein and 90 explicit water molecules embedded in the electrostatic field of all remaining water molecules within a distance of 11.3 angstrom. These configurations include 305 atoms and 842 valence electrons, justifying the use of a semi-empirical approach. The electronic spectrum is then calculated using the INDO/CIS method. The solvatochromic shift of fluorescein in water, compared with in isolation, is calculated using the discrete and explicit solvent models. The use of electrostatically embedded explicit water molecules, in INDO/CIS calculations, gives a good description of the spectral shift of the fluorescein dianion in aqueous environment. The results are verified to converge both statistically and with respect to the number of explicit solvent molecules used.

Probing the (6,7)Li nucleon densities through a new break-up process approach

In this work we present a double folding optical model analysis of new near-barrier quasi-elastic experimental data for the (6,7)Li + (120)Sn systems. From the analysis, it was possible to confirm the ground-state nucleon densities assumed for the weakly bound (6,7)Li isotopes. The apparent discrepancies between the experimental densities and those based on Dirac-Hartree-Fock Bogoliubov (DHB) calculations were removed. A new approach that simulates the projectile break-up and a positive polarization from couplings of (6,7)Li bound states with the continuum was considered in the reaction mechanism. (C) 2010 Elsevier B.V. All rights reserved.

An imaginary potential with universal normalization for dissipative processes in heavy-ion reactions

In this work we present new coupled channel calculations with the Sao Paulo potential (SPP) as the bare interaction, and an imaginary potential with system and energy independent normalization that has been developed to take into account dissipative processes in heavy-ion reactions. This imaginary potential is based on high-energy nucleon interaction in nuclear medium. Our theoretical predictions for energies up to approximate to 100 MeV/nucleon agree very well with the experimental data for the p, n + nucleus, (16)O + (27)Al, (16)O + (60)Ni, (58)Ni + (124)Sn, and weakly bound projectile (7)Li + (120)Sn systems. (C) 2008 Elsevier B.V. All rights reserved.

Oxide surface modification: Synthesis and characterization of zirconia-coated alumina

Four aluminas were used as Supports for impregnation with a zirconium oxide with the aim to achieve a coating, without phase separation, between Support and modifier. The Supports were impregnated with different concentrations Of zirconium aqueous resin, obtained through the polymeric precursor method. After impregnation the samples were calcined and then characterized by XRD, which led to identification of crystalline zirconia in different concentrations from each support used. Using a simple geometric model the maximum amount Of Surface modifier Oxide required for the complete coating of a support with a layer of unit cells was estimated. According to this estimate, only the support should be identified below the limit proposed and crystalline zirconium oxide Should be identified above this limit when a complete coating is reached. The results obtained From XRD agree with the estimated values and to confirm the coating, the samples were also characterized by EDS/STEM, HRTEM, XPS, and XAS. The results showed that the zirconium oxide oil the Surface of alumina Support reached the coating in the limit of 15 Zr nm(-2), without the formation of the ZrO(2) phase. (c) 2009 Elsevier Inc. All rights reserved.

Early Changes in Gene Expression Induced by Tobacco Smoke: Evidence for the Importance of Estrogen within Lung Tissue

Lung cancer is the leading cause of cancer deaths in the United States, surpassing breast cancer as the primary cause of cancer-related mortality in women. The goal of the present study was to identify early molecular changes in the lung induced by exposure to tobacco smoke and thus identify potential targets for chemoprevention. Female A/J mice were exposed to either tobacco smoke or HEPA-filtered air via a whole-body exposure chamber (6 h/d, 5 d/wk for 3, 8, and 20 weeks). Gene expression profiles of lung tissue from control and smoke-exposed animals were established using a 15K cDNA microarray. Cytochrome P450 1b1, a phase I enzyme involved in both the metabolism of xenobiotics and the 4-hydroxylation of 17 beta-estradiol (E(2)), was modulated to the greatest extent following smoke exposure. A panel of 10 genes were found to be differentially expressed in control and smoke-exposed lung tissues at 3, 8, and 20 weeks (P < 0.001). The interaction network of these differentially expressed genes revealed new pathways modulated by short-term smoke exposure, including estrogen metabolism. In addition, E(2) was detected within murine lung tissue by gas chromatography-coupled mass spectrometry and immunohistochemistry. Identification of the early molecular events that contribute to lung tumor formation is anticipated to lead to the development of promising targeted chemopreventive therapies. In conclusion, the presence of E2 within lung tissue when combined with the modulation of cytochrome P450 1b1 and other estrogen metabolism genes by tobacco smoke provides novel insight into a possible role for estrogens in lung cancer. Cancer Prev Res; 3(6); 707-17. (C) 2010 AACR.

3D face computational photography using PCA spaces

In this paper, we present a 3D face photography system based on a facial expression training dataset, composed of both facial range images (3D geometry) and facial texture (2D photography). The proposed system allows one to obtain a 3D geometry representation of a given face provided as a 2D photography, which undergoes a series of transformations through the texture and geometry spaces estimated. In the training phase of the system, the facial landmarks are obtained by an active shape model (ASM) extracted from the 2D gray-level photography. Principal components analysis (PCA) is then used to represent the face dataset, thus defining an orthonormal basis of texture and another of geometry. In the reconstruction phase, an input is given by a face image to which the ASM is matched. The extracted facial landmarks and the face image are fed to the PCA basis transform, and a 3D version of the 2D input image is built. Experimental tests using a new dataset of 70 facial expressions belonging to ten subjects as training set show rapid reconstructed 3D faces which maintain spatial coherence similar to the human perception, thus corroborating the efficiency and the applicability of the proposed system.

Identification of genes associated with local aggressiveness and metastatic behavior in soft tissue tumors

Soft tissue tumors represent a group of neoplasia with different histologic and biological presentations varying from benign, locally confined to very aggressive and metastatic tumors. The molecular mechanisms responsible for such differences are still unknown. The understanding of these molecular alterations mechanism will be critical to discriminate patients who need systemic treatment from those that can be treated only locally and could also guide the development of new drugs` against this tumors. Using 102 tumor samples representing a large spectrum of these tumors, we performed expression profiling and defined differentially expression genes that are likely to be involved in tumors that are locally aggressive and in tumors with metastatic potential. We described a set of 12 genes (SNRPD3, MEGF9, SPTAN-1, AFAP1L2, ENDOD1, SERPIN5, ZWINTAS, TOP2A, UBE2C, ABCF1, MCM2, and ARL6IP5) showing opposite expression when these two conditions were compared. These genes are mainly related to cell-cell and cell-extracellular matrix interactions and cell proliferation and might represent helpful tools for a more precise classification and diagnosis as well as potential drug targets.

Density-Profile Processes Describing Biological Signaling Networks: Almost Sure Convergence to Deterministic Trajectories

We introduce jump processes in R(k), called density-profile processes, to model biological signaling networks. Our modeling setup describes the macroscopic evolution of a finite-size spin-flip model with k types of spins with arbitrary number of internal states interacting through a non-reversible stochastic dynamics. We are mostly interested on the multi-dimensional empirical-magnetization vector in the thermodynamic limit, and prove that, within arbitrary finite time-intervals, its path converges almost surely to a deterministic trajectory determined by a first-order (non-linear) differential equation with explicit bounds on the distance between the stochastic and deterministic trajectories. As parameters of the spin-flip dynamics change, the associated dynamical system may go through bifurcations, associated to phase transitions in the statistical mechanical setting. We present a simple example of spin-flip stochastic model, associated to a synthetic biology model known as repressilator, which leads to a dynamical system with Hopf and pitchfork bifurcations. Depending on the parameter values, the magnetization random path can either converge to a unique stable fixed point, converge to one of a pair of stable fixed points, or asymptotically evolve close to a deterministic orbit in Rk. We also discuss a simple signaling pathway related to cancer research, called p53 module.

A CASSCF/MRCI Study of the Low-Lying Electronic States of the BeS Molecule

Accurate potential energy curves, dipole moment functions, dissociation energies, and molecular constants for several low-lying singlet and triplet electronic states of BeS were investigated using the CASSCF/MRCI methodology, and the cc-pV5Z basis set for beryllium, and the aug-cc-pV(5+d) Z set for sulfur. Besides presenting improved results for the three lowest lying states, this study presents the first theoretical characterization of another set of nine excited states so far unknown experimentally. Our results are sufficiently accurate to reliably guide the experimental search and characterization of these states, and also to confirm the experimental assignment of the B(1)Sigma(+) excited state. (C) 2010 Wiley Periodicals, Inc. Int J Quantum Chem 111: 1694-1700, 2011

Biotransformation of alpha-Bromoacetophenones by the Marine Fungus Aspergillus sydowii

The biotransformation reactions of alpha-bromoacetophenone (1), p-bromo-alpha-bromoacetophenone (2), and p-nitro-alpha-bromoacetophenone (3) by whole cells of the marine fungus Aspergillus sydowii Ce19 have been investigated. Fungal cells that had been grown in artificial sea water medium containing a high concentration of chloride ions (1.20 M) catalysed the biotransformation of 1 to 2-bromo-1-phenylethanol 4 (56%), together with the alpha-chlorohydrin 7 (9%), 1-phenylethan-1,2-diol 9 (26%), acetophenone 10 (4%) and phenylethanol 11 (5%) identified by GC-MS analysis. In addition, it was observed that the enzymatic reaction was accompanied by the spontaneous debromination of 1 to yield alpha-chloroacetophenone 5 (9%) and alpha-hydroxyacetophenone 6 (18%) identified by GC-FID analysis. When 2 and 3 were employed as substrates, various biotransformation products were detected but the formation of halohydrins was not observed. It is concluded that marine fungus A. sydowii Ce19 presents potential for the biotransformations of bromoacetophenone derivatives.

A theoretical study on the XeF(2) molecule

A relativistic four-component study was performed for the XeF(2) molecule by using the Dirac-Coulomb (DC) Hamiltonian and the relativistic adapted Gaussian basis sets (RAGBSs). The comparison of bond lengths obtained showed that relativistic effects on this property are small (increase of only 0.01 angstrom) while the contribution of electron correlation, obtained at CCSD(T) or CCSD-T levels, is more important (increase of 0.05 angstrom). Electron correlation is also dominant over relativistic effects for dissociation energies. Moreover, the correlation-relativity interaction is shown to be negligible for these properties. The electron affinity, the first ionization potential and the double ionization potential are obtained by means of the Fock-space coupled cluster (FSCC) method, resulting in DC-CCSD-T values of 0.3 eV, 12.5 eV and 32.3 eV, respectively. Vibrational frequencies and some anharmonicity constants were also calculated under the four-component formalism by means of standard perturbation equations. All these molecular properties are, in general, ill satisfactory agreement with available experimental results. Finally, a partition in terms of charge-charge flux-dipole flux (CCFDF) contributions derived by means of the quantum theory of atoms in molecules (QTAIM) in non-relativistic QCISD(FC)/3-21G* calculations was carried out for XeF(2) and KrF(2). This analysis showed that the most remarkable difference between both molecules lies on the charge flux contribution to the asymmetric stretching mode, which is negligible in KrF(2) but important in XeF(2). (c) 2008 Elsevier B.V. All rights reserved.

Axial ligand influence on geometries, charge distributions and electronic structures of iron tetraazamacrocycle [Fe((II))TIM(X)(Y)](2+) complexes assessed by Density Functional Theory

We employed the Density Functional Theory along with small basis sets, B3LYP/LANL2DZ, for the study of FeTIM complexes with different pairs of axial ligands (CO, H(2)O, NH(3), imidazole and CH(3)CN). These calculations did not result in relevant changes of molecular quantities as bond lengths, vibrational frequencies and electronic populations supporting any significant back-donation to the carbonyl or acetonitrile axial ligands. Moreover, a back-donation mechanism to the macrocycle cannot be used to explain the observed changes in molecular properties along these complexes with CO or CH(3)CN. This work also indicates that complexes with CO show smaller binding energies and are less stable than complexes with CH(3)CN. Further, the electronic band with the largest intensity in the visible region (or close to this region) is associated to the transition from an occupied 3d orbital on iron to an empty pi* orbital located at the macrocycle. The energy of this Metal-to-Ligand Charge Transfer (MLCT) transition shows a linear relation to the total charge of the macrocycle in these complexes as given by Mulliken or Natural Population Analysis (NPA) formalisms. Finally, the macrocycle total charge seems to be influenced by the field induced by the axial ligands. (C) 2011 Elsevier Ltd. All rights reserved.