Affiliation:
1. University of Science and Technology of China Department of Physics, , Hefei, Anhui 230026, China
Abstract
Molecular motors play important roles in cellular activities. To understand their working mechanism, multiscale methods are needed to perform studies hierarchically. In this chapter, we first show how to utilize molecular dynamics (MD) simulations to explore the conformational change of motor proteins in their working cycle. A dual-basin structure-based coarse-grained model is developed to overcome the bottleneck of traditional all-atomistic MD. Second, we provide detailed explanations of how to use a discrete stochastic model named “tug-of-war” (TOW) to extend the study to the mesoscopic level. The TOW model captures the competition among motors well and quantitatively describes the transport process in several micrometers along cytoskeletons. Finally, hands-on exercises are provided to guide readers to build the MD model and the stochastic model step by step.
Publisher
AIP Publishing LLCMelville, New York