Schütte and Sarich offer this computational modeling text, explaining the mathematical background of Markov state models (MSMs) with an eye toward their use in simulating large biomolecules and aggregates. The conceptual outline of MSMs is presented in chapter 1, followed by an overview of existing molecular dynamics models and how to usefully consolidate them in one mathematical framework. The core of the technique is the analysis of metastable states and using them to simplify the computational problem. This is done using transfer operators and a spectral approach to metastability. The text covers how to construct MSMs using these tools, and also how to use the resulting models to obtain information about transition pathways. Detail is presented at a level geared toward graduate students with interest in theoretical mathematics supplementing their primary discipline. Annotation ©2014 Ringgold, Inc., Portland, OR (protoview.com)