Molecular shuttles based on the motor protein kinesin and microtubule filaments have the potential to extend the lab-on-a-chip paradigm to nanofluidics by enabling the active, directed and selective transport of molecules and nanoparticles. Based on experimentally determined parameters, in particular the trajectory persistence length of a microtubule gliding on surface-adhered kinesin motors, we developed a Monte-Carlo simulation, which models the transport properties of guiding structures, such as channels, rectifiers and concentrators, and reproduces the properties of several experimentally realized systems. Our tool facilitates the rational design of individual guiding structures as well as whole networks, and can be adapted to the simulation of other nanoscale transport systems.

The design of nanoscale transport systems utilizing motor proteins as engines has advanced rapidly. Here, actin/myosin- and microtubule/kinesin-based molecular shuttles are compared with respect to their requirements for track designs. To this end, the trajectory persistence length of actin filaments gliding on myosin-coated surfaces has been experimentally determined to be equal to 8.8 +/- 2 microm. This measurement complements an earlier determination of the trajectory persistence length of microtubules gliding on kinesin-coated surfaces and enables a comparison of the accessible track designs for kinesin and myosin motor-powered systems. Despite the 200-fold smaller stiffness of actin filaments compared to that of microtubules, the dimensions of myosin tracks for actin filaments have to be quite similar to the dimensions of kinesin tracks for microtubules (radii larger than 200 nm and widths smaller than 0.9 microm compared to 600 nm and 19 microm). The difference in gliding speed is shown to require additional consideration in the design of track modules.

We present an extended computer simulation method which allows in silico design and testing of guiding tracks for molecular shuttles powered by kinesin motors. The simulation reproduced molecular shuttle movements under external forces and dissociation of shuttles from guiding track surfaces. The simulation was validated by comparing the simulation results with the corresponding experimental ones. Using the simulation, track designers can change guiding track designs, choose guiding methods, tune the strength of external forces, and test the module performance. This simulation would significantly reduce the effort expended in designing guiding tracks for molecular shuttles powered by kinesin motors.