Hydration dynamics data analysis

Description of the mechanics of elastin requires the understanding of two interlinked but distinct physical processes the development of entropic elastic force and the occurrence of hydrophobic association. Elementary statistical-mechanical analysis of AFM single-chain force-extension data of elastin model molecules identifies damping of internal chain dynamics on extension as a fundamental source of entropic elastic force and eliminates the requirement of random chain networks. For elastin and its models, this simple analysis is substantiated experimentally by the observation of mechanical resonances in the dielectric relaxation and acoustic absorption spectra, and theoretically by the dependence of entropy on frequency of torsion-angle oscillations, and by classical molecular-mechanics and dynamics calculations of relaxed and extended states of the P-spiral description of the elastin repeat, (GVGVP) . The role of hydrophobic hydration in the mechanics of elastin becomes apparent under conditions of isometric contraction. 

Recent reviews from this Laboratory provide an overview of the literature of MD simulations on DNA oligomers through 1993 (27) and theoretical and computational aspects of DNA hydration (28) and counterion atmosphere (29). References to the most recent literature can be found in (30). Experimental data for comparison with MD results are available for crystal structures in the Nucleic acids Data Bank (NDB) (31), and for NMR structure in a review by Ulyanov and James (52). The research described in this article is directed towards understanding the dynamical structure of the various right-handed helical forms of DNA, their deformations and interconversions. The canonical A and B structures of DNA are shown for reference in Figure 1. The A and B forms are distinguishable in three major ways the displacement of nucleotide base pairs from the helix axis, the inclination of base pairs with respect to the helix axis, and sugar puckers. Details on these and other structural features of DNA relevant to MD analysis is readily available (33). 

Vosko SL, Wilk L, Nusair M (1980) Accurate spin-dependent electron liquid correlation energies for local spin density calculations a critical analysis. Can J Phys 58 1200-1211 Wagman DD, Evans WH, Parker VB, Schumm RH, Halow I, Bailey SM, Chumey KL, Nuttall, RL (1982) The NBS Tables of chemical thermodynamic properties, selected values for inorganic and cl and c2 organic substances in SI units. J Chem Phys Ref Data (Supplement 2) 11 1-329 Wallen SL, Palmer BJ, Fulton JL (1998) The ion-pairing and hydration stracture of NP in supercritical water at 425 degrees C determined by X-ray absorption fine stracture and molecular dynamics studies. J Chem Phys 108 4039-4046... 

This coarse-grained molecular dynamics model helped consolidate the main features of microstructure formation in CLs of PEFCs. These showed that the final microstructure depends on carbon particle choices and ionomer-carbon interactions. While ionomer sidechains are buried inside hydrophilic domains with a weak contact to carbon domains, the ionomer backbones are attached to the surface of carbon agglomerates. The evolving structural characteristics of the catalyst layers (CL) are particularly important for further analysis of transport of protons, electrons, reactant molecules (O2) and water as well as the distribution of electrocatalytic activity at Pt/water interfaces. In principle, such meso-scale simulation studies allow relating of these properties to the selection of solvent, carbon (particle sizes and wettability), catalyst loading, and level of membrane hydration in the catalyst layer. There is still a lack of explicit experimental data with which these results could be compared. Versatile experimental techniques have to be employed to study particle-particle interactions, structural characteristics of phases and interfaces, and phase correlations of carbon, ionomer, and water in pores. 

Westlund et al. have studied the hydration of Peroxiredoxin 5 protein combining MD simulations and data from the water proton Nuclear Magnetic Relaxtion Dispersion (NMRD) experiments using simulated orientational order parameters and residence times of buried water molecules as parameters in the NMRD model. They find the dynamics of the water molecules associated with the protein, both with short or long residence time, to be complex and beyond the reach of the NMRD analysis alone. This again supports the use of MD and NMR in combination to obtain a more detailed analysis. 

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