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Molecular dynamics simulations of the Z-DNA hexamer 5BrdC-dG-5BrdC-dG-5BrdC-dG were performed at several temperatures between 100 K and 300 K. Above 250 K, a strong sequence-dependent flexibility in the nucleic acid is observed, with the guanine sugar and the phosphate of GpC sequences much more mobile than the cytosine sugar and phosphate of CpG sequences. At 300 K, the hexamer is in dynamic equilibrium between several Z forms, including the crystallographically determined ZI and ZII forms. The local base-pair geometry, however, is not very variable, except for the roll of the base-pairs. The hexamer molecular dynamics trajectories have been used to test the restrained parameter crystallographic refinement model for nucleic acids. X-ray diffraction intensities corresponding to observed diffraction data were computed. The average structures obtained from the simulations were then refined against the calculated intensities, using a restrained least-squares program developed for nucleic acids in order to analyse the effects of the refinement model on the derived quantities. In general, the temperature dependence of the atomic fluctuations determined directly from the refined Debye-Waller factors is in reasonably good agreement with the results obtained by calculating the atomic fluctuations directly from the Z-DNA molecular dynamics trajectories. The agreement is best for refinement of temperature factors without restraints. At the highest temperature studied (300 K), the effect of the refinement on the most mobile atoms (phosphates) is to significantly reduce the mean-square atomic fluctuations estimated from the refined Debye-Waller factors below the actual values (less than (delta r)2 greater than congruent to 0.5 A2). Analysis of the temperature-dependence of the mean-square atomic fluctuations provides information concerning the conformational potential within which the atoms move. The calculated temperature-dependence and anharmonicity of the Z-DNA helix are compared with the results observed for proteins. The average structures from the simulations were refined against the experimental X-ray intensities. It is found that low-temperature molecular dynamics simulations provide a useful tool for optimizing the refinement of X-ray structures.

Abstract: Geosynthetic Clay Liners (GCLs) are often used in waste disposal facilities. In order to act as a barrier as cover or bottom liner, GCLs must hydrate and swell under a confining pressure. According to the French Committee for Geosynthetics (), the gravimetric water content of the bentonite must be at least 100%. GCLs are commonly installed at their initial bentonite water content (around 10–15%), for practical reasons and ease of installation. Therefore, the duration of the hydration period (vapour and liquid migration from the subgrade) appears to be an important issue in terms of confining performance. This question was addressed during laboratory and field experiments performed on a natural sodium bentonite GCL and aimed at examining the influence of several parameters: subgrade (sand versus clay), temperature and confining pressure. Results illustrate the high influence of the subgrade permeability and water content on the bentonite final water content level and hydration kinetic. As could be expected, sandy soils allow a faster hydration and higher water content than clayey soils for a same period of observation. The hydration rate and the final gravimetric water content at equilibrium both increase significantly when temperature rises. But a low temperature, such as tested during the experiments (5 °C), drastically slows down the rate of hydration but also the final water content, whatever the material. The vertical stress also appears to influence the hydration rate by providing a better contact between the GCML and the soil. The water content at equilibrium appears to be not improved by that confining stress whatever the materials and the temperature. [Copyright &y& Elsevier]