sets [@ZXCang:2016b].

The objective of this paper is threefold. First, the main objective is to provide a review of some widely used geometric, topological and graph theory apparatuses for the modeling and analysis of biomolecular data. We keep our description concise, elementary and accessible to upper level undergraduate students in mathematics and most researchers in computational biophysics. We point out some open problems and potential topics in our discussions. Our goal is to provide a reference for mathematicians who are interested in mathematical molecular bioscience and biophysics (MMBB), an emergent field in mathematics [@Wei:2016], and for biophysicists and theoreticians who are interested in mathematical foundations of many theoretical approaches in molecular biology and biophysics. Obviously, our topic selection is limited by our knowledge, experience and understanding, and for the same reason, we might have missed many important results and references on the selected topics as well. Additionally, inspired by the success of QCT and persistent homology, the density filtration for Hessian matrix eigenvalue maps and molecular curvature maps has been introduced. Both maps are constructed from molecular rigidity density obtained via a discrete to continuum mapping (DCM) technique, which transfers atomic information in a molecule to atomic density distribution, a 