Hydrophobic and ionic-interactions in bulk and confined water with implications for collapse and folding of proteins

Water and water-mediated interactions determine thermodynamic and kinetics of protein folding, protein aggregation and self-assembly in confined spaces. To obtain insights into the role of water in the context of folding problems, we describe computer simulations of a few related model systems. The dynamics of collapse of eicosane shows that upon expulsion of water the linear hydrocarbon chain adopts an ordered helical hairpin structure with 1.5 turns. The structure of dimer of eicosane molecules has two well ordered helical hairpins that are stacked perpendicular to each other. As a prelude to studying folding in confined spaces we used simulations to understand changes in hydrophobic and ionic interactions in nano droplets. Solvation of hydrophobic and charged species change drastically in nano water droplets. Hydrophobic species are localized at the boundary. The tendency of ions to be at the boundary where water density is low increases as the charge density decreases. Interaction between hydrophobic, polar, and charged residue are also profoundly altered in confined spaces. Using the results of computer simulations and accounting for loss of chain entropy upon confinement we argue and then demonstrate, using simulations in explicit water, that ordered states of generic amphiphilic peptide sequences should be stabilized in cylindrical nanopores

Long-Lived Localized Field Configurations in Small Lattices: Application to Oscillons

Long-lived localized field configurations such as breathers, oscillons, or more complex objects naturally arise in the context of a wide range of nonlinear models in different numbers of spatial dimensions. We present a numerical method, which we call the {\it adiabatic damping method}, designed to study such configurations in small lattices. Using 3-dimensional oscillons in $\phi^4$ models as an example, we show that the method accurately (to a part in 10^5 or better) reproduces results obtained with static or dynamically expanding lattices, dramatically cutting down in integration time. We further present new results for 2-dimensional oscillons, whose lifetimes would be prohibitively long to study with conventional methods.Comment: LaTeX, 8 pages using RevTeX. 6 PostScript figures include