Models of Molecular Motors

Molecular motors in living cells are complex protein assemblies that perform mechanical tasks, such as intracellular transport, ion pumping, DNA replication and protein synthesis. Distinct from macroscopic, man-made machines, molecular motors work in a very noisy environment, where thermal fluctuations are significant and probably important to the operation of the motor. Molecular machines are also capable of transforming chemical energy directly into mechanical work, unlike man-made heat engines that need an extra step (heat).

To help understanding the basic physical principles that govern molecular motors it is helpful to develop relatively simple model systems. The goal of such models is not to replicate the usually very complex biological reality, but to create controlled environments that can teach us about the basic principles that may be in common to all nanoscale, thermal machines.

Our group uses both numerical and experimental methods to create such models, many of which are related to ratchets and Brownian motors.

Numerical Models
In collaboration with the group of Martin Zuckermann at SFU, we perform Brownian dynamics simulations that help us guide our experimental work. For instance, we explored a flashing ratchet that acts on the internal degrees of freedom of a molecule (a polymer).

Experimental Models
We currently develop experiments to realize molecular motors powered by either an electrostatic ratchet potential, or a time-dependent optical potential created by scanning-line optical traps. In each case, the time-dependent potential acts on a construct of DNA molecules and polystyrene beads. These constructs (motors) are much larger than biological motors, such that it is possible in principle to watch them in real time. Yet the motors are small enough for thermal fluctuations to play an important role.

Movie Clips (by Matthew Downton)
Freely-jointed chain polymer in a flashing ratchet (PRE 73, 011909 (2006)).
Dimer in a flashing ratchet.

Key Researchers at UO
Erin Craig (theory)
Brian Long (experiment)
Ben Lopez (experiment)

Collaborators
Martin Zuckermann, Simon Fraser University , Canada
Matthew Downton, Simon Fraser University , Canada
Michael Plischke, Simon Fraser University , Canada
Jonas Tegenfeldt , Nanometer Structure Consortium, Lund University

Representative Publications

E. M. Craig, M.J. Zuckermann, and H. Linke: Mechanical coupling in flashing ratchets.
cond-mat/0602097

M. T. Downton, M.J. Zuckermann, E. M. Craig, M. Plischke and H. Linke: Single-polymer motor: a simulation study.
Phys. Rev. E 73, 011909 (2006) Supplementary movies

H. Linke, M. T. Downton and M.J. Zuckermannn: Performance Characteristics of Brownian motors
Chaos 15 , 026111 (2005)

Funding
NSF Career Award PHY0239764 (2003 - 2008)

Links on Molecular Motors
Motorhome
Vale lab
Bustamante lab

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