  Despite significant fluctuation under thermal noise, biological machines in
cells perform their tasks with exquisite precision. Using molecular simulation
of a coarse-grained model and theoretical arguments we envisaged how kinesin, a
prototype of biological machines, generates force and regulates its dynamics to
sustain persistent motor action. A structure based model, which can be
versatile in adapting its structure to external stresses while maintaining its
native fold, was employed to account for several features of kinesin dynamics
along the biochemical cycle. This analysis complements our current
understandings of kinesin dynamics and connections to experiments. We propose a
thermodynamic cycle for kinesin that emphasizes the mechanical and regulatory
role of the neck-linker and clarify issues related the motor directionality,
and the difference between the external stalling force and the internal tension
responsible for the head-head coordination. The comparison between the
thermodynamic cycle of kinesin and macroscopic heat engines highlights the
importance of structural change as the source of work production in
biomolecular machines.
