Abstract
This paper presents a multibody dynamics approach to the modeling, simulation and analysis of motor protein dynamic behavior. Usually proteins are modeled as a collection of a small number of particles, oftentimes only two particles, with spring-like connections between them. However, these simple particle models potentially omit interactions and dynamics between the unmodeled particles and the environment that may be important. Multibody dynamics models can be used to address this issue. However, widely used techniques for analyzing particle models may not be applicable to multibody models. Herein the validity of the small mass assumption, which is central to the analysis of particle models, is examined in detail using a simplified multibody model of the molecular motor protein Myosin V.
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