Home About us Contact
|
Home About us Contact | ||
|
|
||
Previous Experimental (previous + experimental)
Terms modified by Previous Experimental Selected AbstractsTheoretical study of the interaction between a high-valent manganese porphyrin oxyl-(hydroxo)-Mn(IV)-TMPyP and double-stranded DNAJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2003Philippe Arnaud Abstract Cationic porphyrin derivatives such as meso-tetrakis(4- N -methylpyridinium)porphyrin, TMPyP, have been shown to interact with double-stranded DNA. The manganese derivative, Mn(III)-TMPyP, activated by an oxygen donor like potassium monopersulfate, provides an efficient DNA-cleaving system. Previous experimental work1 has shown that DNA cleavage by the Mn(III)-TMPyP/KHSO5 system was due to an oxidative attack, within the minor groove of B-DNA, at the C5, or C1, carbons of deoxyribose units. The aim of this study was to use molecular modeling to elucidate the specificity of the interactions between the transient active species oxyl-Mn(IV)-TMPyP and the DNA target. Geometric parameters, charges, and force field constants consistent with the AMBER 98 force field were calculated by DFT methods. Molecular modeling (mechanics and dynamic simulations) were performed for oxyl-(hydroxo)-Mn(IV)-TMPyP bound in the minor groove of the dodecamer d(5,-TCGTCAAACCGC)-d(5,-GCGGTTTGACGA). Geometry, interactions, and binding energy of the metalloporphyrin located at the A.T triplet region of the dodecamer were analyzed. These studies show no significant structural change of the DNA structure upon ligand binding. Mobility of the metalloporphyrin in the minor groove was restrained by the formation of a hydrogen bond between the hydroxo ligand trans to the metal-oxyl and a DNA phosphate, restricting the access of the oxyl group to the (pro-S) H atom at C5,. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 797,805, 2003 [source] Large eddy simulation (2D) of spatially developing mixing layer using vortex-in-cell for flow field and filtered probability density function for scalar fieldINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, Issue 1 2006J. K. Wang Abstract A large eddy simulation based on filtered vorticity transport equation has been coupled with filtered probability density function transport equation for scalar field, to predict the velocity and passive scalar fields. The filtered vorticity transport has been formulated using diffusion-velocity method and then solved using the vortex method. The methodology has been tested on a spatially growing mixing layer using the two-dimensional vortex-in-cell method in conjunction with both Smagorinsky and dynamic eddy viscosity subgrid scale models for an anisotropic flow. The transport equation for filtered probability density function is solved using the Lagrangian Monte-Carlo method. The unresolved subgrid scale convective term in filtered density function transport is modelled using the gradient diffusion model. The unresolved subgrid scale mixing term is modelled using the modified Curl model. The effects of subgrid scale models on the vorticity contours, mean streamwise velocity profiles, root-mean-square velocity and vorticity fluctuations profiles and negative cross-stream correlations are discussed. Also the characteristics of the passive scalar, i.e. mean concentration profiles, root-mean-square concentration fluctuations profiles and filtered probability density function are presented and compared with previous experimental and numerical works. The sensitivity of the results to the Schmidt number, constant in mixing frequency and inflow boundary conditions are discussed. Copyright © 2005 John Wiley & Sons, Ltd. [source] Range and strength of intermolecular forces for van der Waals complexes of the type H2Xn -Rg, with X = O, S and n = 1,2INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2010Patrícia R. P. Barreto Abstract This study is intended as a continuation of previous experimental and theoretical works on the systems H2O-Rg, H2S-Rg, H2O2 -Rg, and H2S2 -Rg, where Rg = He, Ne, Ar, Kr, Xe. For the H2O-Rg and H2S-Rg systems, molecular and atomic polarizabilities have been calculated and from them, using phenomenological correlation formulas modeling the dispersion-repulsion (van der Waals) forces, the isotropic interaction parameters have been determined and compared with experimental data from this laboratory. For the H2O2 -Rg and H2S2 -Rg systems, the molecular polarizabilities have been calculated and used in correlation formulas to predict well depths and positions of van der Waals forces and a comparison made with the corresponding potential energy surfaces calculated in previous works. The approach correctly predicts the interaction parameters, except for H2O and H2O2 with the heavier rare gases. The correlation formulas have been then extended to include an attractive induction contribution accounting for the interaction between the permanent molecular dipole moment and the instantaneous induced atomic dipole moment, to improve the predicted parameters for H2O and H2O2 -Ar, Kr and Xe. The agreement with experimental and theoretical data is improved but the predicted data still underestimate the interaction. This is probably due to the presence of a significant non van der Waals contribution to the interaction for the heavier gases, as suggested by analogy with the previously studied water-Rg case. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Theoretical calculations of transition probabilities and oscillator strengths for Ti III and Ti IVINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 2 2009Tian-Yi Zhang Abstract Due to the complicated electronic configuration of atoms and ions of the transition metal elements, the studies for properties such as transition probabilities and oscillator strengths for these atoms and ions are not systematic. Because of the existence in a variety of stellar objects and wide use in the field of astrophysics, titanium has long been of interest for many researchers. In this article within the Weakest Bound Electron Potential Model (WBEPM) theory, comprehensive set of calculations for transition probabilities and oscillator strengths for Ti III and Ti IV are performed. Many of our results had no previous experimental or theoretical values, so these predictive results could be of some value to the workers in this field. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Biodiversity effects on ecosystem functioning: emerging issues and their experimental test in aquatic environmentsOIKOS, Issue 3 2004Paul S. Giller Recent experiments, mainly in terrestrial environments, have provided evidence of the functional importance of biodiversity to ecosystem processes and properties. Compared to terrestrial systems, aquatic ecosystems are characterised by greater propagule and material exchange, often steeper physical and chemical gradients, more rapid biological processes and, in marine systems, higher metazoan phylogenetic diversity. These characteristics limit the potential to transfer conclusions derived from terrestrial experiments to aquatic ecosystems whilst at the same time provide opportunities for testing the general validity of hypotheses about effects of biodiversity on ecosystem functioning. Here, we focus on a number of unique features of aquatic experimental systems, propose an expansion to the scope of diversity facets to be considered when assessing the functional consequences of changes in biodiversity and outline a hierarchical classification scheme of ecosystem functions and their corresponding response variables. We then briefly highlight some recent controversial and newly emerging issues relating to biodiversity-ecosystem functioning relationships. Based on lessons learnt from previous experimental and theoretical work, we finally present four novel experimental designs to address largely unresolved questions about biodiversity-ecosystem functioning relationships. These include (1) investigating the effects of non-random species loss through the manipulation of the order and magnitude of such loss using dilution experiments; (2) combining factorial manipulation of diversity in interconnected habitat patches to test the additivity of ecosystem functioning between habitats; (3) disentangling the impact of local processes from the effect of ecosystem openness via factorial manipulation of the rate of recruitment and biodiversity within patches and within an available propagule pool; and (4) addressing how non-random species extinction following sequential exposure to different stressors may affect ecosystem functioning. Implementing these kinds of experimental designs in a variety of systems will, we believe, shift the focus of investigations from a species richness-centred approach to a broader consideration of the multifarious aspects of biodiversity that may well be critical to understanding effects of biodiversity changes on overall ecosystem functioning and to identifying some of the potential underlying mechanisms involved. [source] Structural and dynamical properties of the Ge(001)/Sb(2×1) surfacePHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 11 2004H. M. Tütüncü Abstract The structural properties of the Ge(001)/Sb(2×1) surface were investigated by using the density functional theory. The calculated structural parameters for this surface are in good agreement with previous experimental and theoretical results. In addition to structural properties, we present the complete phonon spectrum of this surface as calculated from first principles employing density functional theory. We have compared the phonon spectrum of this surface with that of the clean Ge(001)(2×1) surface in detail. We have found that adsorption of Sb results in several characteristic phonon modes. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Instabilities and bifurcations in lid-driven cavity flowsPROCEEDINGS IN APPLIED MATHEMATICS & MECHANICS, Issue 1 2003Hendrik C. Kuhlmann Dr. The three-dimensional flow of an incompressible Newtonian fluid in a rectangular slab is calculated numerically using a pseudo-spectral method. The fluid motion is driven by two facing sidewalls which can move in parallel or anti-parallel directions. Examples for bifurcations from two-dimensional to three-dimensional flows are given for spanwise periodic systems. For a comparison with previous experimental results rigid end walls are also considered. Differences between periodic and rigid end conditions are highlighted. [source] | |||||||||||||