Averaging over Discrete Conformations

To address this point, Scarsdale et al.47 used a two-state model to build a penalty function. Two noninteracting copies of the oligosaccharide head group of globoside were simulated at once, and the penalty function was based on the weighted average of the two molecules. This weighting was, in turn, based on 

This approach is certainly better than trying to model data by a single average conformation, but it seems to be of limited applicability. It is only in small molecules that one is likely to have a small number of well-characterized conformations and the choice of initial conformations seems quite arbitrary. 

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Consider a two-dimensional, scalar conservation law of the form (1) with solution u(t,x). Within the finite volume framework, each discrete value of the function u is viewed as a cell average U( over a cell. The advantage of the finite volume approach is, that any kind of mesh can be used, i.e., the shape of the control volume can be chosen arbitrarily. Here, we work with a conforming triangulation T with cells Te T, = for which the... 

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