Characterizing Structural Transitions Using Localized Free Energy Landscape Analysis

Structural changes in molecules are frequently observed during biological processes like replication, transcription and translation. These structural changes can usually be traced to specific distortions in the backbones of the macromolecules involved. Quantitative energetic characterization of such distortions can greatly advance the atomic-level understanding of the dynamic character of these biological processes.Molecular dynamics simulations combined with a variation of the Weighted Histogram Analysis Method for potential of mean force determination are applied to characterize localized structural changes for the test case of cytosine (underlined) base flipping in a GTCAGCGCATGG DNA duplex. Free energy landscapes for backbone torsion and sugar pucker degrees of freedom in the DNA are used to understand their behavior in response to the base flipping perturbation. By simplifying the base flipping structural change into a two-state model, a free energy difference of upto 14 kcal/mol can be attributed to the flipped state relative to the stacked Watson-Crick base paired state. This two-state classification allows precise evaluation of the effect of base flipping on local backbone degrees of freedom.The calculated free energy landscapes of individual backbone and sugar degrees of freedom expectedly show the greatest change in the vicinity of the flipping base itself, but specific delocalized effects can be discerned upto four nucleotide positions away in both 5' and 3' directions. Free energy landscape analysis thus provides a quantitative method to pinpoint the determinants of structural change on the atomic scale and also delineate the extent of propagation of the perturbation along the molecule. In addition to nucleic acids, this methodology is anticipated to be useful for studying conformational changes in all macromolecules, including carbohydrates, lipids, and proteins

On applying the ideal adsorbed solution theory to multicomponent adsorption equilibria of dissolved organic components on activated carbon

Multicomponent adsorption equilibria of organic components from aqueous solutions on activated carbons were measured and the applicability of the ideal adsorbed solution (IAS) theory was tested. Systematic deviations between experiments and theory were observed. Adsorbed phase activity coefficients which account for these deviations proved to be thermodynamically inconsistent. However, the calculation of spreading pressure in the IAS theory requires extrapolation of single solute isotherms to zero concentration. A correction of extrapolation errors was determined by fitting binary equilibrium data to the IAS theory. For a mixture of N components, N – 1 constants have to be obtained from binary mixtures of N – 1 components with a reference component. For the adsorption of 3 chemically non-interacting organic solutes constants derived from two binary systems allow the prediction of the third binary system as well as of the ternary system. The method is successful only if chemical interactions of the components in the adsorbed phase can be excluded

Breakthrough curves for single solutes in beds of activated carbon with a broad pore-size distribution : I. Mathematical models of breakthrough curves in beds of activated carbon

A model proposed for the calculation of breakthrough curves (BTCs) in the adsorption of organic solutes from aqueous solution on activated carbons takes into account external diffusion as well as internal diffusion and adsorption in two discrete pore zones. Parameters of the equilibrium adsorption in the two pore zones are to be evaluated from independent equilibrium measurements and are input data for the column calculation. Parametric investigations show the influences of external diffusion, the value of surface diffusivity, the concentration dependence of the diffusion constant, entrance concentration and of the ratio of adsorption capacities and diffusivities in the two pore zones on the shape of the BTCs. It is concluded that the existence of two pore zones with individual adsorption capacities and different diffusivities must be included in the model if BTCs of the type often observed in active carbon columns are to be accurately described

Infections cutanéo-muqueuses communautaires acquises (CA) à Staphylococcus aureus et à Streptococcus pyogenes (aspects diagnostiques et thérapeutiques)

CAEN-BU Médecine pharmacie (141182102) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

Etude sur les prescriptions de neuroleptiques chez des patients psychotiques au centre hospitalier Sainte-Anne (état des lieux en Aquitaine et analyse pharmaco-économique)

BORDEAUX2-BU Santé (330632101) / SudocSudocFranceF

Equilibrium adsorption of two-component organic solutes from aqueous solutions on activated carbon

The adsorption equilibria of the mixtures phenol-indol, indol-p-nitrophenol (pNP), α-picoline-phenol from aqueous solution on activated carbon, mainly Hydraffin 71 and BHT 023/82 have been studied. Significant displacement of one solute by the other was observed. The designation of the more strongly adsorbed component depends on the relative concentration of the two solutes in the mixture and on the pH. Predictive equations for calculating mixture equilibria solely on the basis of single solute isotherms do not agree well with the experimental values; the introduction of empirical parameters determined by curve-fitting is necessary. A multi-Redlich-Peterson equation is derived, which yields a satisfactory reprensentation of most of the present binary solute adsorption data