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.

Equations for the Drag Force and Aerodynamic Roughness Length of Urban Areas with Random Building Heights

We use a conceptual model to investigate how randomly varying building heights within a city affect the atmospheric drag forces and the aerodynamic roughness length of the city. The model is based on the assumptions regarding wake spreading and mutual sheltering effects proposed by Raupach (Boundary-Layer Meteorol 60:375-395, 1992). It is applied both to canopies having uniform building heights and to those having the same building density and mean height, but with variability about the mean. For each simulated urban area, a correction is determined, due to height variability, to the shear stress predicted for the uniform building height case. It is found that u (*)/u (*R) , where u (*) is the friction velocity and u (*R) is the friction velocity from the uniform building height case, is expressed well as an algebraic function of lambda and sigma (h) /h (m) , where lambda is the frontal area index, sigma (h) is the standard deviation of the building height, and h (m) is the mean building height. The simulations also resulted in a simple algebraic relation for z (0)/z (0R) as a function of lambda and sigma (h) /h (m) , where z (0) is the aerodynamic roughness length and z (0R) is z (0) found from the original Raupach formulation for a uniform canopy. Model results are in keeping with those of several previous studies.