Compartmentalized Molecular Machines
A R T I C L E S
the past decade physicists have developed formal theoretical
mechanisms, deeply rooted in nonequilibrium statistical me-
chanics, which explain how the directional transport of Brownian
particles can occur from periodic changes in a potential energy
surface (e.g., by applying an oscillating electric field).21,22 Many
different possible types of these theoretical “Brownian ratchet”
mechanisms have been suggested, including energy ratchets,
information ratchets, flashing ratchets, tilting ratchets, and
rocking ratchets.22 These mechanisms have been successfully
applied to the development of transport and separation devices
for mesoscopic particles and macromolecules, microfluidic
pumping, and quantum and electronic applications23,24 and have
also been shown to successfully account for the general
principles that govern the operation of complex biological
motors.24,25 However, to date it is not known how such
theoretical mechanisms correlate with the changes that occur
in molecular structure during the operation of biological
machines. What do individual peptide fragments do in order to
bring about transport of an ion or molecule by a Brownian
ratchet mechanism and why? We wondered whether examining
how these principles can be applied to some much less
sophisticated (in terms of function as well as structure) synthetic
molecular machines could tell us something about how they
might apply to more complex systems, both artificial and natural.
be considered to continuously fluctuate between the two stations.
However, even for a molecular shuttle with two different
stations, at equilibrium no net task can be performed by these
movements. This is a consequence of the “Principle of Detailed
Balance”;26 at equilibrium transitions between any two states
take place in either direction at the same rate so that no flux is
generated. This rules out the maintenance of equilibria by cyclic
(20) Stimuli-induced shuttling has been used to control a number of different
properties. See: Fluorescence switching: (a) Pe´rez, E. M.; Dryden, D. T.
F.; Leigh, D. A.; Teobaldi, G.; Zerbetto, F. J. Am. Chem. Soc. 2004, 126,
12210-12211. (b) Wang, Q.-C.; Qu, D.-H.; Ren, J.; Chen, K.; Tian, H.
Angew. Chem., Int. Ed. 2004, 43, 2661-2665. (c) Qu, D.-H.; Wang, Q.-
C.; Ren, J.; Tian, H. Org. Lett. 2004, 6, 2085-2088. (d) Qu, D.-H.; Wang,
Q.-C.; Tian, H. Mol. Cryst. Liq. Cryst. 2005, 430, 59-65. (e) Leigh, D.
A.; Morales, M. A. F.; Pe´rez, E. M.; Wong, J. K. Y.; Saiz, C. G.; Slawin,
A. M. Z.; Carmichael, A. J.; Haddleton, D. M.; Brouwer, A. M.; Buma,
W. J.; Wurpel, G. W. H.; Leo´n, S.; Zerbetto, F. Angew. Chem., Int. Ed.
2005, 44, 3062-3067. (f) Qu, D.-H.; Wang, Q.-C.; Tian, H. Angew. Chem.,
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Statistical Balance of a Dynamically Exchangeable
Substrate or Quantity (The Principle of Detailed
Balance)
If we ignore the normally small population of rings on the
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