Ramachandran-type Plots for Glycosidic Linkages: Examples from Molecular Dynamics Simulations using the Glycam06 Force Field

The goals of this article are to (1) provide further validation of the Glycam06 force field, specifically for its use in implicit solvent molecular dynamic (MD) simulations, and (2) to present the extension of G.N. Ramachandran's idea of plotting amino acid phi and psi angles to the glycosidic phi, psi, and omega angles formed between carbohydrates. As in traditional Ramachandran plots, these carbohydrate Ramachandran-type (carb-Rama) plots reveal the coupling between the glycosidic angles by displaying the allowed and disallowed conformational space. Considering two-bond glycosidic linkages, there are 18 possible conformational regions that can be defined by (α, ϕ, ψ) and (β, ϕ, ψ), whereas for three-bond linkages, there are 54 possible regions that can be defined by (α, ϕ, ψ, ω) and (β, ϕ, ψ, ω). Illustrating these ideas are molecular dynamic simulations on an implicitly hydrated oligosaccharide (700 ns) and its eight constituent disaccharides (50 ns/disaccharide). For each linkage, we compare and contrast the oligosaccharide and respective disaccharide carb-Rama plots, validate the simulations and the Glycam06 force field through comparison to experimental data, and discuss the general trends observed in the plots.

Strong Dynamical Heterogeneity and Universal Scaling in Driven Granular Fluids

Large-scale simulations of two-dimensional bidisperse granular fluids allow us to determine spatial correlations of slow particles via the four-point structure factor S-4 (q, t). Both cases, elastic (epsilon = 1) and inelastic (epsilon < 1) collisions, are studied. As the fluid approaches structural arrest, i.e., for packing fractions in the range 0.6 <= phi <= 0.805, scaling is shown to hold: S-4 (q, t)/chi(4)(t) = s(q xi(t)). Both the dynamic susceptibility chi(4)(tau(alpha)) and the dynamic correlation length xi(tau(alpha)) evaluated at the alpha relaxation time tau(alpha) can be fitted to a power law divergence at a critical packing fraction. The measured xi(tau(alpha)) widely exceeds the largest one previously observed for three-dimensional (3d) hard sphere fluids. The number of particles in a slow cluster and the correlation length are related by a robust power law, chi(4)(tau(alpha)) approximate to xi(d-p) (tau(alpha)), with an exponent d - p approximate to 1.6. This scaling is remarkably independent of epsilon, even though the strength of the dynamical heterogeneity at constant volume fraction depends strongly on epsilon.