Revealing Free Energy Landscape from MD Data via Conditional Angle Partition Tree

Deciphering the free energy landscape of biomolecular structure space is crucial for understanding many complex molecular processes, such as protein-protein interaction, RNA folding, and protein folding. A major source of current dynamic structure data is Molecular Dynamics (MD) simulations. Several methods have been proposed to investigate the free energy landscape from MD data, but all of them rely on the assumption that kinetic similarity is associated with global geometric similarity, which may lead to unsatisfactory results. In this paper, we proposed a new method called Conditional Angle Partition Tree to reveal the hierarchical free energy landscape by correlating local geometric similarity with kinetic similarity. Its application on the benchmark alanine dipeptide MD data showed a much better performance than existing methods in exploring and understanding the free energy landscape. We also applied it to the MD data of Villin HP35. Our results are more reasonable on various aspects than those from other methods and very informative on the hierarchical structure of its energy landscape.

A tree-based dictionary learning framework

We propose a new outline for adaptive dictionary learning methods for sparse encoding based on a hierarchical clustering of the training data. Through recursive application of a clustering method, the data is organized into a binary partition tree representing a multiscale structure. The dictionary atoms are defined adaptively based on the data clusters in the partition tree. This approach can be interpreted as a generalization of a discrete Haar wavelet transform. Furthermore, any prior knowledge on the wanted structure of the dictionary elements can be simply incorporated. The computational complexity of our proposed algorithm depends on the employed clustering method and on the chosen similarity measure between data points. Thanks to the multiscale properties of the partition tree, our dictionary is structured: when using Orthogonal Matching Pursuit to reconstruct patches from a natural image, dictionary atoms corresponding to nodes being closer to the root node in the tree have a tendency to be used with greater coefficients.