Erin M. Craig

Effect of time delay on feedback control of a flashing ratchet

It was recently shown that the use of feedback control can improve the performance of a flashing ratchet. We investigate the effect of a time delay in the implementation of feedback control in a closed-loop collective flashing ratchet, using Langevin dynamics simulations. Surprisingly, for a large ensemble, a well-chosen delay time improves the ratchet performance by allowing the system to synchronize into a quasi-periodic stable mode of oscillation that reproduces the optimal average velocity for a periodically flashing ratchet. For a small ensemble, on the other hand, finite delay times significantly reduce the benefit of feedback control for the time-averaged velocity, because the relevance of information decays on a time scale set by the diffusion time of the particles. Based on these results, we establish that the experimental use of feedback control is realistic.

Mechanochemical model for myosin V

A rigorous numerical test of a hypothetical mechanism of a molecular motor should model explicitly the diffusive motion of the motors degrees of freedom as well as the transition rates between the motors chemical states. We present such a Brownian dynamics, mechanochemcial model of the coarse-grain structure of the dimeric, linear motor myosin V. Compared with run-length data, our model provides strong support for a proposed strain-controlled gating mechanism that enhances processivity. We demonstrate that the diffusion rate of a detached motor head during motor stepping is self-consistent with known kinetic rate constants and can explain the motors key performance features, such as speed and stall force. We present illustrative and realistic animations of motor stepping in the presence of thermal noise. The quantitative success and illustrative power of this type of model suggest that it will be useful in testing our understanding of a range of biological and synthetic motors.

Realization of a Feedback Controlled Flashing Ratchet

A flashing ratchet transports diffusive particles using a time-dependent, asymmetric potential. The particle speed is predicted to increase when a feedback algorithm based on the particle position is used. We have experimentally realized such a feedback ratchet using an optical line trap, and observed that use of feedback increases velocity by up to an order of magnitude. We compare two different feedback algorithms for small particle numbers, and find good agreement with simulations. We also find that existing algorithms can be improved to be more tolerant to feedback delay times.

Mechanical coupling in flashing ratchets

We consider the transport of rigid objects with internal structure in a flashing ratchet potential by investigating the overdamped behavior of a rodlike chain of evenly spaced point particles. In one dimension, analytical arguments show that the velocity can reverse direction multiple times in response to changing the size of the chain or the temperature of the heat bath. The physical reason is that the effective potential experienced by the mechanically coupled objects can have a different symmetry than that of individual objects. All analytical predictions are confirmed by Brownian dynamics simulations. These results may provide a route to simple, coarse-grained models of molecular motor transport that incorporate an objects size and rotational degrees of freedom into the mechanism of transport.