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Control at molecular (nano) scale has been extensively studied emphasizing protein dynamics. Different electro-chemo-mechanical processes have been examined researching biological systems. This paper concentrates the attention on motion of molecular motors. We report the motion dynamics of nanoscale proteins (size in the range of 10 nm). The cornerstone principles of the energy conversion and dynamic motion are based on the multi-degree-of-freedom complementary electrochemomechanical bonding. We enhance the thermal ratchet probability-based concept. This bioinspired concept results in highly nonlinear equations of motion that describe temporal evolution. The studied molecular machines perform transport guaraneeing functionality of living cells. Thermal fluctuations are the major source of energy for these machines. They transport biological materials and ions, build proteins, attain motility of the cell, engaged in actuation and activation, etc. Fluctuation-driven transport is studied applying the Brownian ratchet principle. This concept provides the understanding of how electrochemical energy converted into mechanical energy. The importance of Brownian motion is its versatility in explaining a wide range of biological processes and examining the energy conversion at molecular scale. This paper proposes a realistic molecular control mechanism utilizing the multi-degree-of-freedom complementary electrochemomechanical bonding and considering multi-molecules interactive dynamics.