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In this work, a general dynamic model was proposed to simulate the dynamic motion of microtubules driven by dynein motors, which is of importance to the design of potential nano-bio machines composed of dynein motors and microtubules. The model was developed based on Newton's law of motion. By incorporating a DPD technique, the general model was applied to simulate the unidirectional motion of microtubule. The functions of dyneins and their coordination with each other, which plays an important role in the motion of microtubules, were studied. By taking into account the bending energy of microtubules, we extended the general model to study possible mechanisms responsible for the microtubule-microtubule and microtubule-wall interactions, which are essential to the design of optimal track patterns for potential nanomachine systems. This study helps to evaluate the influence of bending and rotation on microtubule joining processes, involving bumping force, bending moment and torque generation. Finally, a phenomenal modeling study based on the Monte Carlo method, was conducted to investigate the self-organization of microtubules driven by dynein motors and identify out key parameters that control the self-organized movement of microtubules, giving crucial information for nano device design. This modeling study helps to clarify several important issues regarding the interaction between dynein motors and microtubules as a power transfer medium, which provides important information for the development of potential nanobio-machines using dynein as a biological motor.