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The Kinesin family of motor proteins are involved in a variety of cellularprocesses that transport materials and generate force. With recent advances inexperimental techniques, such as optical tweezers which can probe individualmolecules, there has been an increasing interest in understanding themechanisms by which motor proteins convert chemical energy into mechanicalwork. Here we present a mathematical model for the chemistry and threedimensional mechanics of the Kinesin motor protein which captures many of theforce dependent features of the motor. For the elasticity of the tether thatattaches cargo to the motor we develop a method for deriving the non-linearforce-extension relationship from optical trap data. For the Kinesin heads,cargo, and microscope stage we formulate a three dimensional Brownian Dynamicsmodel that takes into account excluded volume interactions. To efficientlycompute statistics from the model an algorithm is proposed that uses a two stepprotocol that separates the simulation of the mechanical features of the modelfrom the chemical kinetics of the model. Using this approach for a beadtransported by the motor, the force dependent average velocity and randomnessparameter are computed and compared with the experimental data.

A Brownian Dynamics Model of Kinesin in Three Dimensions Incorporating the Force-Extension Profile of the Coiled-Coil Cargo Tether