arXiv subjects

Shoichi Toyabe

Publications and source records attributed to Shoichi Toyabe.

15 recordsLinked to original sources

arXiv2025

Experimental demonstration of kinetic proofreading inherited in ligation-based information replication

We experimentally demonstrate that information replication by templated ligation of DNA strands inherits a kinetic proofreading mechanism and achieves significant error suppression through cascade replication. A simple simulation model derived from the experimental results shows that templated ligation has a significant advantage over replication by polymerization for error suppression of long strands. Specifically, longer chains show lower error rates, significantly distinct from the chain-growth polymerization where errors typically accumulate with chain length. This mechanism provides a plausible route for high-fidelity replication in prebiotic chemistry and illustrates how physical principles such as nonequilibrium kinetics and network architecture can drive reliable molecular information replication. The approach also offers new strategies for error suppression in biotechnology.

physics.bio-ph↗

arXiv2025

Acceleration of enzymatic reaction-diffusion kinetics by intermediate state

Biological molecular motors are high-performance nanomachines that convert chemical energy into mechanical motion via chemomechanical coupling. Their reaction cycles typically comprise a series of intermediate chemical states between the initial and final primary states. However, the influence of these intermediate states on motor performance has not yet been fully explored. In this study, we investigate the impact of intermediate states on the motor kinetics using a reaction-diffusion model. In most cases, the intermediate states accelerate the motor by lowering the effective barrier height. This acceleration is particularly pronounced when an external load is applied to the motor, implying the practical importance of the intermediate states. The intermediate states can also slow down the reaction in some cases, such as the slow reaction limit with asymmetric kinetics. Our findings provide practical insights into the design principles behind the high performance of biological molecular motors, as well as the development of efficient artificial molecular motors.

physics.bio-ph↗

arXiv2025

Asymmetric enzyme kinetics of F1-ATPase induced by rotation-assisted substrate binding

We demonstrate asymmetric enzyme kinetics of a biomolecular motor F1-ATPase between synthesis and hydrolysis of adenosine triphosphate (ATP). Our experiments show that ATP hydrolysis follows Michaelis-Menten kinetics, but ATP synthesis, which is an F1-ATPase's primary biological role, deviates from it. Specifically, the synthesis rate is sustained even at low substrate concentrations. Analysis of a theoretical model consistent with the experimental results reveals that ATP synthesis implements a rotation-assisted mechanism, in which a limited binding rate at low substrate concentration is partially compensated for by rotation to an angle where the binding rate is high. The results may imply that F1-ATPase implements a regulatory mechanism of enhancing substrate binding for ATP synthesis.

physics.bio-ph↗

arXiv2025

Efficiently driving F$_1$ molecular motor in experiment by suppressing nonequilibrium variation

F$_1$-ATPase (F$_1$) is central to cellular energy transduction. Forcibly rotated by another motor F$_\mathrm{o}$, F$_1$ catalyzes ATP synthesis by converting mechanical work into chemical free energy stored in the molecule ATP. The details of how F$_\mathrm{o}$ drives F$_1$ are not fully understood; however, evaluating efficient ways to rotate F$_1$ could provide fruitful insights into this driving since there is a selective pressure to improve efficiency. Here, we show that rotating F$_1$ with an angle clamp is significantly more efficient than a constant torque. Our experiments, combined with theory and simulation, indicate that the angle clamp significantly suppresses the nonequilibrium variation that contributes to the futile dissipation of input work.

physics.bio-ph↗

arXiv2025

Experimentally achieving minimal dissipation via thermodynamically optimal transport

Optimal transport theory, originally developed in the 18th century for civil engineering, has since become a powerful optimization framework across disciplines, from generative AI to cell biology. In physics, it has recently been shown to set fundamental bounds on thermodynamic dissipation in finite-time processes. This extends beyond the conventional second law, which guarantees zero dissipation only in the quasi-static limit and cannot characterize the inevitable dissipation in finite-time processes. Here, we experimentally realize thermodynamically optimal transport using optically trapped microparticles, achieving minimal dissipation within a finite time. As an application to information processing, we implement the optimal finite-time protocol for information erasure, confirming that the excess dissipation beyond the Landauer bound is exactly determined by the Wasserstein distance - a fundamental geometric quantity in optimal transport theory. Furthermore, our experiment achieves the bound governing the trade-off between speed, dissipation, and accuracy in information erasure. To enable precise control of microparticles, we develop scanning optical tweezers capable of generating arbitrary potential profiles. Our work establishes an experimental approach for optimizing stochastic thermodynamic processes. Since minimizing dissipation directly reduces energy consumption, these results provide guiding principles for designing high-speed, low-energy information processing.

cond-mat.stat-mech↗

arXiv2022

Optimal Control of the F${_1}$-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.

cond-mat.stat-mech↗

arXiv2021

Optimal rectification without forward-current suppression by biological molecular motor

We experimentally showed that biological molecular motor F$_1$-ATPase (F$_1$) implements an optimal rectification mechanism. F$_1$ hardly suppresses adenosine triphosphate (ATP) synthesis, which is the F$_1$'s physiological role while inhibiting unfavorable hydrolysis of ATP. This optimal rectification is a high contrast to a simple ratchet model, where the inhibition of the backward current is inevitably accompanied by the suppression of the forward current. The detailed analysis of single-molecule trajectories demonstrated a novel but simple rectification mechanism of F$_1$ with parallel landscapes and asymmetric transition rates.

physics.bio-ph↗

arXiv2020

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.

cond-mat.stat-mech↗

arXiv2019

Cooperative ligation breaks sequence symmetry and stabilizes early molecular replication

Each living species carries a complex DNA sequence that determines their unique features and functionalities. It is generally assumed that life started from a random pool of oligonucleotides sequences, generated by a prebiotic polymerization of nucleotides. The mechanism that initially facilitated the emergence of sequences that code for the function of the first species from such a random pool of sequences remains unknown. It is a central problem of the origin of life. An interesting option would be a self-selection mechanism by spontaneous symmetry breaking. Initial concentration fluctuations of specific sequence motifs would have been amplified and outcompeted less abundant sequences, enhancing the signal to noise to replicate and select functional sequences. Here, we demonstrate with experimental and theoretical findings that templated ligation would provide such a self-selection. In templated ligation, two adjacent single sequences strands are chemically joined when a third complementary strand sequence brought them in close proximity. This simple mechanism was a likely side-product of a prebiotic polymerization chemistry once the strands reach the length to form double stranded species. As shown here, the ligation gave rise to a nonlinear replication process by the cooperative ligation of matching sequences which self-promoted their own elongation. This led to a cascade of enhanced template binding and faster ligation reactions. A requirement was the reshuffling of the strands by thermal cycling, enabled for example by microscale convection. Assuming that templated ligation was driven by the same chemical mechanism that generated prebiotic polymerization of oligonucleotides, the mechanism could function as a missing link between polymerization and the self-stabilized replication, offering a pathway to the autonomous emergence of Darwinian evolution for the origin of life.

physics.bio-ph↗

arXiv2019

Evaluation of the duty ratio of bacterial flagellar motor by a dynamic load control

Bacterial flagellar motor is one of the most complex and sophisticated nano machineries in nature. A duty ratio $D$ is a fraction of time that the stator and the rotor interact and is a fundamental property to characterize the motor but remains to be determined. It is known that the stator units of the motor bind to and dissociate from the motor dynamically to control the motor torque depending on the load on the motor. At low load where the kinetics such as a proton translocation speed limits the rotation rate, the dependency of the rotation rate on the number of stator units $N$ infers $D$; the dependency becomes larger for smaller $D$. Contradicting observations supporting both the small and large $D$ have been reported. A dilemma is that it is difficult to explore a broad range of $N$ at low load because the stator units easily dissociate, and $N$ is limited to one or two at vanishing load. Here, we develop an electrorotation method to dynamically control the load on the flagellar motor of {\it Salmonella} with a calibrated magnitude of the torque. By instantly reducing the load for keeping $N$ high, we observed that the speed at low load depends on $N$, implying a small duty ratio. We recovered the torque-speed curves of individual motors and evaluated the duty ratio to be $0.14 \pm 0.04$ from the correlation between the torque at high load and the rotation rate at low load.

physics.bio-ph↗

arXiv2015

Single molecule thermodynamics of ATP synthesis by F$_1$-ATPase

F$_\mathrm{o}$F$_1$-ATP synthase is a factory for synthesizing ATP in virtually all cells. Its core machinery is the subcomplex F$_1$-motor (F$_1$-ATPase) and performs the reversible mechanochemical coupling. Isolated F$_1$-motor hydrolyzes ATP, which is accompanied by unidirectional rotation of its central $γ$-shaft. When a strong opposing torque is imposed, the $γ$-shaft rotates in the opposite direction and drives the F$_1$-motor to synthesize ATP. This mechanical-to-chemical free-energy transduction is the final and central step of the multistep cellular ATP-synthetic pathway. Here, we determined the amount of mechanical work exploited by the F$_1$-motor to synthesize an ATP molecule during forced rotations using methodology combining a nonequilibrium theory and single molecule measurements of responses to external torque. We found that the internal dissipation of the motor is negligible even during rotations far from a quasistatic process.

physics.bio-ph↗

arXiv2011

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.

physics.bio-ph↗

arXiv2010

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.

cond-mat.stat-mech↗

arXiv2010

Nonequilibrium energetics of a single F1-ATPase molecule

Molecular motors drive mechanical motions utilizing the free energy liberated from chemical reactions such as ATP hydrolysis. Although it is essential to know the efficiency of this free energy transduction, it has been a challenge due to the system's microscopic scale. Here, we evaluate the single-molecule energetics of a rotary molecular motor, F1-ATPase, by applying a recently derived nonequilibrium equality together with an electrorotation method. We show that the sum of the heat flow through the probe's rotational degree of freedom and the work against external load is almost equal to the free energy change per a single ATP hydrolysis under various conditions. This implies that F1-ATPase works at an efficiency of nearly 100% in a thermally fluctuating environment.

cond-mat.stat-mech↗

arXiv2007

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.

cond-mat.stat-mech↗