Using normal mode analysis in teaching mathematical modeling to biology students

University of Chicago, BSCD, 924 E 57th St, Chicago, IL 60637, USA

¹ E-mail: dkon@uchicago.edu

Abstract

Linear oscillators are used for modeling a diverse array of natural systems, for instance acoustics, materials science, and chemical spectroscopy. In this paper I describe simple models of structural interactions in biological molecules, known as elastic network models, as a useful topic for undergraduate biology instruction in mathematical modeling. These models use coupled linear oscillators to model the fluctuations of molecular structures around the equilibrium state. I present many learning activities associated with building and understanding these models, ranging from analytical to computational. I provide a number of web resources where students can obtain structural data, perform calculations, and suggest research directions for independent projects.