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Kinetic asymmetry allows macromolecular catalysts to drive an information ratchet
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Thermodynamics of Non-Equilibrium Processes for Chemists with a Particular Application to Catalysis
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Small systems found throughout physics, chemistry, and biology manifest striking Thermodynamics describes energy exchange processes of macroscopic In particular, in a nonequilibrium small system, thermal fluctuations can lead to. Specific applications of nonequilibrium thermodynamics have been studied in analysis of cell signaling, describing transport processes, activation kinetics are now part of the drug-design tools of pharmaceutical chemistry.
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Several examples drawn from the recent literature, including a catenane-based chemically driven molecular rotor and a synthetic molecular assembler or pump, are discussed. Living systems require continual input of energy. Some of this energy is used to create and to maintain structure and function, and the rest is wasted dissipated. Examples of phenomena relevant for macromolecules that occur in the presence of energy flow, and by which order arises, include directed motion 2 , molecular adaptation 3 , and assembly of high free-energy structures 4.
There has been great progress recently in understanding how energy is absorbed and harnessed by molecular systems brought about by remarkable achievements in the design and synthesis of molecules that operate away from chemical equilibrium 5. It is becoming evident that thermodynamically non-equilibrium phenomena can be best understood in the context of microscopic reversibility 6.
There is no requirement that the averages of the fluxes depend linearly on the externally applied forces. Few systems would obey this criterion for even moderate applied forces. Instead, from the single-molecule perspective, the requirement is that the local fluxes i. This condition is met if the motion of a single molecule is over-damped and governed by a single potential an energy landscape , a condition fulfilled by essentially all chemically, but not optically 14 , driven molecular systems in solution.
A major point of the present perspective article can be summarized succinctly: at thermodynamic equilibrium the distribution among states of a system is determined solely by the free energies of the states and there are no net fluxes between the states; away from thermodynamic equilibrium the deviation of the distribution from the values that would pertain at equilibrium, as well as the fluxes between the states, is determined by the kinetic asymmetry of the system, i.
As the environment of a macromolecule is driven far from equilibrium the macromolecule tends to occupy states of greatest kinetic, not thermodynamic, stability, and the adaptation to non-equilibrium conditions is independent of the free-energies of the states themselves.
go to site Three phrases occur time and time again in this perspective article—information ratchet, kinetic stability, and kinetic asymmetry. Let us clarify these concepts by comparing accomplishment of a macroscopic task with accomplishing a similar task in the microscopic world. Consider Fig.
In the macroscopic world the brick could be pushed from the white to black section of the lowest step. This process would dissipate energy owing to friction between the brick and step. The brick could then be lifted to the next step, an energy input that, in principle, could be accomplished reversibly. Following elevation to the next step the brick would be pushed from the white to black section on the second step, once again dissipating energy because of friction, and then reversibly lifted to the third step to complete the task.
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The intrinsically irreversible steps are those in which the brick is pushed on the flat parts of the steps against the friction between the brick and step. To minimize dissipation maximize efficiency we would have to minimize this friction.
Comparison between a macroscopic task and a microscopic information ratchet. Comparison of a moving a brick up a staircase in the macroscopic world, in which losses through friction are inevitable, and b an information ratchet appropriate for description of a molecular machine in the microscopic world where diffusion provides a mechanism for motion without loss owing to friction but in which the second law forbids net directed motion without the input of energy, and c how this can be described in terms of the four state mechanism for a minimal Brownian machine.
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A similar task in the microscopic world can be accomplished in a very different way that utilizes thermal noise and diffusion Fig. In this example a microscopic brick, positionally blurred because of diffusion, starts on the white section of the bottom stair with the gates in configuration g1.
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