We wish to determine the full energy landscapes for RNA tertiary structure formation and protein secondary structures. We wish to develop theory as close to analytic as possible, that gives partition functions of biomolecules. We will use the energy landscapes to predict stable non-native states, conformational switching, cooperative transitions, and folding transitions. Ultimately we aim to predict biological function. As well, energy landscapes will have applications in determining the stability of proteins. This can be used in determining for which amino acid sequence of the beta-amyloid protein are aggregates most stable. We are in the preliminary stages of testing a new method for enumerating conformations of polymers with given contact constraints. The polymer is modeled as a network of self avoiding walks. The approach can be completely generalized to handle complex non-local polymer interactions and works in 3 dimensional lattice models. We hope to use this method to handle non-local protein interactions during folding.
