Proteins and other large biomolecules can be modeled as mechanical linkages, reminiscent in many ways of articulated robot arms. To simulate their motions, the existing mathematical theories and computational tools do not scale up: the entire process of folding or unfolding of a protein is a problem that poses formidable computational challenges. Useful information about the molecule’s “potential to flex” can be gathered through rigidity analysis, and in turn this can shed light on questions concerning its function.
Students engaged in this project explore questions directly motivated by protein geometry, and participate in the design and development of prototype computer simulations. The underlying mathematics includes graph theory, computational geometry, rigidity theory and kinematics.