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Molecular dynamics simulations of liquid ethanol at four thermodynamic states ranging from T ) 173 K to T ) 348 K were carried out using the transferable OPLS potential model of Jorgensen (J. Phys. Chem. 1986Chem. , 90, 1276. Both static and dynamic properties are analyzed. The resulting properties show an overall agreement with available experimental data. Special attention is paid to the hydrogen bonds and to their influence on the molecular behavior. Results for liquid ethanol are compared with those for methanol in earlier computer simulation studies.

The formation of DNA loops by the binding of proteins and protein complexes at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination and replication. Important thermodynamic concepts underlie the assembly of macromolecular complexes on looped DNA. The effects that this process has on the properties of gene regulation extend beyond the traditional view of DNA looping as a mechanism to increase the affinity of regulatory molecules for their cognate sites. Recent developments indicate that DNA looping can also lead to the suppression of cell-to-cell variability, the control of transcriptional noise, and the activation of cooperative interactions on demand.

The structure of a fully hydrated mixed (saturated/polyunsaturated) chain lipid bilayer in the biologically relevant liquid crystalline phase has been examined by performing a molecular dynamics study. The model membrane, a 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (SDPC, 18:0/22:6 PC) lipid bilayer, was investigated at constant (room) temperature and (ambient) pressure, and the results obtained in the nanosecond time scale reproduced quite well the available experimental data. Polyunsaturated fatty acids are found in high concentrations in neuronal and retinal tissues and are essential for the development of human brain function. The docosahexaenoic fatty acid, in particular, is fundamental for the proper function of the visual receptor rhodopsin. The lipid bilayer order has been investigated through the orientational order parameters. The water-lipid interface has been explored thoroughly in terms of its dimensions and the organization of the different components. Several types of interactions occurring in the system have been analyzed, specifically, the water-hydrocarbon chain, lipid-lipid and lipid-water interactions. The distribution of dihedral angles along the chains and the molecular conformations of the polyunsaturated chain of the lipids have also been studied. Special attention has been focused on the microscopic (molecular) origin of the effects of polyunsaturations on the different physical properties of membranes.