Biomolecular Topology: Modelling and Analysis

With the great advancement of experimental tools, a tremendous amount of biomolecular data has been generated and accumulated in various databases. The high dimensionality, structural complexity, the nonlinearity, and entanglements of biomolecular data, ranging from DNA knots, RNA secondary structures, protein folding configurations, chromosomes, DNA origami, molecular assembly, to others at the macromolecular level, pose a severe challenge in their analysis and characterization. In the past few decades, mathematical concepts, models, algorithms, and tools from algebraic topology, combinatorial topology, computational topology, and topological data analysis, have demonstrated great power and begun to play an essential role in tackling the biomolecular data challenge. In this work, we introduce biomolecular topology, which concerns the topological problems and models originated from the biomolecular systems. More specifically, the biomolecular topology encompasses topological structures, properties and relations that are emerged from biomolecular structures, dynamics, interactions, and functions. We discuss the various types of biomolecular topology from structures (of proteins, DNAs, and RNAs), protein folding, and protein assembly. A brief discussion of databanks (and databases), theoretical models, and computational algorithms, is presented. Further, we systematically review related topological models, including graphs, simplicial complexes, persistent homology, persistent Laplacians, de Rham—Hodge theory, Yau—Hausdorff distance, and the topology-based machine learning models.