The flagellar motor of Escherichia coli is a bidirectional rotary nano-motor, powered by a transmembrane influx of protons. The maximum speed of rotation is about 300 Hz. The motor rotates either counterclockwise (CCW) or clockwise (CW) and the rotation direction is controlled by a chemotactic protein, CheY-P. Despite extensive structural and functional studies, precise mechanisms regarding the torque generation and the directional switching processes remain unclear. In this work, a bottom-up strategy is proposed and followed to investigate this motor. This strategy, named as a multiscale modeling approach, integrates various publicly available experimental data and ‘state-of-the-art’ molecular modeling methods to build structural models for the two most important parts of the motor, the C ring and the stator. Starting from the primary sequences of the composition proteins of these two substructures, tertiary structures are predicted by means of comparative modeling or de novo prediction when the comparative modeling is not available. Quaternary structures of these proteins’s complexes are then predicted by data-driven protein-protein docking or multiscale molecular dynamics (MD) simulations. Finally, structural models of the C ring at CCW and CW rotational states are constructed by cryo-EM aided assembling methods (constraint search that is based on the multiscale modeling tools and under the constraint of the EM images). In the case of the stator, its composition proteins, MotA and MotB, are assembled by coarse-grained MD simulations. This is the first molecular model based atomistic details for the stator. A new molecular mechanism for rotational switching is proposed based on the structural models of the C ring and the stator. The two states of the C ring display significant differences in the interfaces among the self-assembled FliMs and the orientations of FliG C-terminal domain. Based on protein docking results, a binding site of CheY-P is identified on FliM which is close to the interfaces of FliMs for self-assembling. Thereby, I propose that the CheY-P binding interferes with the interactions between neighboring FliM proteins, and thus, induces ~65° rotation of the FliGc domain with respect to FliM. Subsequently, the interactions between the stator and FliGc domains are altered and the rotation direction is changed. Furthermore, a mechanism accounting for the directed rotation of the flagellar motor is proposed based on systematic MD studies on the dynamics of FliGc. It is found that the C-terminal subdomain of FliGc is capable of rotating by ~180° with respect to the N-terminal subdomain of FliGc. If this dynamics is considered in the framework of the whole C ring, the rotation of the C-terminal subdomain of FliGc exhibits an asymmetric feature. As a result, the C ring is decorated with asymmetric teeth on the outer periphery and hence similar with Feynman’s ratchet. The preference of the motor in CCW rotation or in CW rotation is then explained based on the Feynman’s ratchet model. / published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy