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Irrelevance of the power stroke for the directionality, stopping force, and optimal efficiency of chemically driven molecular machines.

ABSTRACT: A simple model for a chemically driven molecular walker shows that the elastic energy stored by the molecule and released during the conformational change known as the power-stroke (i.e., the free-energy difference between the pre- and post-power-stroke states) is irrelevant for determining the directionality, stopping force, and efficiency of the motor. Further, the apportionment of the dependence on the externally applied force between the forward and reverse rate constants of the power-stroke (or indeed among all rate constants) is irrelevant for determining the directionality, stopping force, and efficiency of the motor. Arguments based on the principle of microscopic reversibility demonstrate that this result is general for all chemically driven molecular machines, and even more broadly that the relative energies of the states of the motor have no role in determining the directionality, stopping force, or optimal efficiency of the machine. Instead, the directionality, stopping force, and optimal efficiency are determined solely by the relative heights of the energy barriers between the states. Molecular recognition--the ability of a molecular machine to discriminate between substrate and product depending on the state of the machine--is far more important for determining the intrinsic directionality and thermodynamics of chemo-mechanical coupling than are the details of the internal mechanical conformational motions of the machine. In contrast to the conclusions for chemical driving, a power-stroke is very important for the directionality and efficiency of light-driven molecular machines and for molecular machines driven by external modulation of thermodynamic parameters.

SUBMITTER: Astumian RD

PROVIDER: S-EPMC4302201 | biostudies-literature | 2015 Jan

REPOSITORIES: biostudies-literature

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Irrelevance of the power stroke for the directionality, stopping force, and optimal efficiency of chemically driven molecular machines.

Astumian R Dean RD

Biophysical journal 20150101 2

A simple model for a chemically driven molecular walker shows that the elastic energy stored by the molecule and released during the conformational change known as the power-stroke (i.e., the free-energy difference between the pre- and post-power-stroke states) is irrelevant for determining the directionality, stopping force, and efficiency of the motor. Further, the apportionment of the dependence on the externally applied force between the forward and reverse rate constants of the power-stroke ...[more]

PMID: 25606678

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Project description:ObjectiveThe objectives of this paper are to 1) construct a new network model compatible with distributed computation, 2) construct the full optimal power flow (OPF) in a distributed fashion so that an effective, non-inferior solution can be found, and 3) develop a scalable algorithm that guarantees the convergence to a local minimum.Existing challengesDue to the nonconvexity of the problem, the search for a solution to OPF problems is not scalable, which makes the OPF highly limited for the system operation of large-scale real-world power grids-"the curse of dimensionality". The recent attempts at distributed computation aim for a scalable and efficient algorithm by reducing the computational cost per iteration in exchange of increased communication costs.MotivationA new network model allows for efficient computation without increasing communication costs. With the network model, recent advancements in distributed computation make it possible to develop an efficient and scalable algorithm suitable for large-scale OPF optimizations.MethodsWe propose a new network model in which all nodes are directly connected to the center node to keep the communication costs manageable. Based on the network model, we suggest a nodal distributed algorithm and direct communication to all nodes through the center node. We demonstrate that the suggested algorithm converges to a local minimum rather than a point, satisfying the first optimality condition.ResultsThe proposed algorithm identifies solutions to OPF problems in various IEEE model systems. The solutions are identical to those using a centrally optimized and heuristic approach. The computation time at each node does not depend on the system size, and Niter does not increase significantly with the system size.ConclusionOur proposed network model is a star network for maintaining the shortest node-to-node distances to allow a linear information exchange. The proposed algorithm guarantees the convergence to a local minimum rather than a maximum or a saddle point, and it maintains computational efficiency for a large-scale OPF, scalable algorithm.

Dataset Information

Irrelevance of the power stroke for the directionality, stopping force, and optimal efficiency of chemically driven molecular machines.

Publications

Irrelevance of the power stroke for the directionality, stopping force, and optimal efficiency of chemically driven molecular machines.

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