Energy Landscapes
The concept of energy landscapes has proven to be of fundamental relevance in investigations of complex disordered systems, from simple spin glass models to biopolymer folding. In this picture, energy is viewed as an explicit function E(S) of underlying conformational degrees of freedom S. The topological structure of the conformation space is determined in terms of the elementary moves that underly the dynamical behavior. Examples are single spin flips in spin glasses, the formation or breaking of a base pair in RNA folding models, or rotation around a bond in a protein folding model.
The geometric properties and topological details of the energy landscape, such as the number of local optima, the saddle points separating them, as well as the size distributions of the basins of attraction, therefore directly influence the dynamics of the underlying system. A thorough understanding of these aspects of geometric landscape structure is thus of wide interest.
The ELL-library provides a platform for generic algorithms to study kinetics and structure of energy landscapes with discrete states. These algorithms need an abstract representation of these states to be applied to a multitude of state instances and their corresponding energy or fitness landscapes.
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Based on the energy landscape library, a set of tools to investigate the structure and topology of RNA energy landscapes has been implemented. These programs allow for:
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For this research topic, we analyze the energy landscape of three-dimensional model proteins. We plan to investigate new techniques for the construction of energy landscape representations and the computation of protein kinetics. We are furthermore interested in the analysis of landscapes of even more complex protein models.
We could show how protein structure prediction helps in the construction of barrier-trees, which represent local minima and energy barriers of the energy landscape. Starting from predicted global optima and structures on the first raised energy levels, we can cover the structure space up to a defined degree.