Bypass mechanism of F1_1-ATPase for asymmetric enzyme kinetics

We discovered novel enzyme kinetics of F$_1$-ATPase, a biomolecular motor that synthesizes and hydrolyzes adenosine triphosphate (ATP), using single-molecule experiments and numerical simulations. The enzyme kinetics of F$_1$-ATPase followed the Michaelis-Menten equation in ATP hydrolysis but deviated from it in ATP synthesis, indicating asymmetric enzyme kinetics between ATP synthesis and hydrolysis. Numerical analysis based on a theoretical model revealed a bypass mechanism underlying asymmetric enzyme kinetics. In particular, we found that the origin of the asymmetric enzyme kinetics lies in the asymmetry of the allosterism, not in the asymmetry of potential shapes. The asymmetric enzyme kinetics may suggest that F$_1$-ATPase is designed to sustain the rate of ATP synthesis while suppressing the futile ATP consumption.Comment: 6 pages, 5 figures + Supplementary Material (2 pages

Experimental characterization of autonomous heat engine based on minimal dynamical-system model

The autonomous heat engine is a model system of autonomous nonequilibrium systems like biological cells, exploiting nonequilibrium flow for operations. As the Carnot engine has essentially contributed to the equilibrium thermodynamics, autonomous heat engine is expected to play a critical role in the challenge of constructing nonequilibrium thermodynamics. However, the high complexity of the engine involving an intricate coupling among heat, gas flow, and mechanics has prevented simple modeling. Here, we experimentally characterized the nonequilibrium dynamics and thermodynamics of a low-temperature-differential Stirling engine, which is a model autonomous heat engine. Our experiments demonstrated that the core engine dynamics are quantitatively described by a minimal dynamical model with only two degrees of freedom. The model proposes a novel concept that illustrates the engine as a thermodynamic pendulum driven by a thermodynamic force. This work will open a new approach to explore the nonequilibrium thermodynamics of autonomous systems based on a simple dynamical system.Comment: 6 pages, 7 figure

Experimental Test of a New Equality: Measuring Heat Dissipation in an Optically Driven Colloidal System

Measurement of energy dissipation in small nonequilibrium systems is generally a difficult task. Recently, Harada and Sasa [Phys.Rev.Lett. 95, 130602(2005)] derived an equality relating the energy dissipation rate to experimentally accessible quantities in nonequilibrium steady states described by the Langevin equation. Here, we show the first experimental test of this new relation in an optically driven colloidal system. We find that this equality is validated to a fairly good extent, thus the irreversible work of a small system is estimated from readily obtainable quantities.Comment: 4 pages, 6 figure

Optimal Control of the F1{_1}-ATPase Molecular Motor

F$_{1}$-ATPase is a rotary molecular motor that \emph{in vivo} is subject to strong nonequilibrium driving forces. There is great interest in understanding the operational principles governing its high efficiency of free-energy transduction. Here we use a near-equilibrium framework to design a non-trivial control protocol to minimize dissipation in rotating F$_{1}$ to synthesize ATP. We find that the designed protocol requires much less work than a naive (constant-velocity) protocol across a wide range of protocol durations. Our analysis points to a possible mechanism for energetically efficient driving of F$_{1}$ \emph{in vivo} and provides insight into free-energy transduction for a broader class of biomolecular and synthetic machines.Comment: 7 pages + SI, Minor revisio

Recovery of state-specific potential of molecular motor from single-molecule trajectory

We have developed a novel method to evaluate the potential profile of a molecular motor at each chemical state from only the probe's trajectory and applied it to a rotary molecular motor F$_1$-ATPase. By using this method, we could also obtain the information regarding the mechanochemical coupling and energetics. We demonstrate that the position-dependent transition of the chemical states is the key feature for the highly efficient free-energy transduction by F$_1$-ATPase.Comment: 5 pages, 5 figure

Information heat engine: converting information to energy by feedback control

In 1929, Leo Szilard invented a feedback protocol in which a hypothetical intelligence called Maxwell's demon pumps heat from an isothermal environment and transduces it to work. After an intense controversy that lasted over eighty years; it was finally clarified that the demon's role does not contradict the second law of thermodynamics, implying that we can convert information to free energy in principle. Nevertheless, experimental demonstration of this information-to-energy conversion has been elusive. Here, we demonstrate that a nonequilibrium feedback manipulation of a Brownian particle based on information about its location achieves a Szilard-type information-energy conversion. Under real-time feedback control, the particle climbs up a spiral-stairs-like potential exerted by an electric field and obtains free energy larger than the amount of work performed on it. This enables us to verify the generalized Jarzynski equality, or a new fundamental principle of "information-heat engine" which converts information to energy by feedback control.Comment: manuscript including 7 pages and 4 figures and supplementary material including 6 pages and 8 figure