arXiv subjects

Kumiko Hayashi

Publications and source records attributed to Kumiko Hayashi.

18 recordsLinked to original sources

arXiv2024

Extreme-value analysis in nano-biological systems: Applications and Implications

Extreme value analysis (EVA) is a statistical method that studies the properties of extreme values of datasets, crucial for fields like engineering, meteorology, finance, insurance, and environmental science. EVA models extreme events using distributions such as Fréchet, Weibull, or Gumbel, aiding in risk prediction and management. This review explores EVA's application to nanoscale biological systems. Traditionally, biological research focuses on average values from repeated experiments. However, EVA offers insights into molecular mechanisms by examining extreme data points. We introduce EVA's concepts with simulations and review its use in studying motor protein movements within cells, highlighting the importance of in vivo analysis due to the complex intracellular environment. We suggest EVA as a tool for extracting motor proteins' physical properties in vivo and discuss its potential in other biological systems. While there have been only a few applications of EVA to biological systems, it holds promise for uncovering hidden properties in extreme data, promoting its broader application in life sciences.

physics.bio-ph↗

arXiv2019

Physical parameters describing neuronal cargo transport by kinesin UNC-104

In this review, we focus on the kinesin-3 family molecular motor protein UNC-104 and its regulatory protein ARL-8. UNC-104, originally identified in Caenorhabditis elegans (C. elegans), has a primary role transporting synaptic vesicle precursors (SVPs). Although in vitro single-molecule experiments have been performed to primarily investigate the kinesin motor domain, these have not addressed the in vivo reality of the existence of regulatory proteins, such as ARL-8, that control kinesin attachment to/detachment from cargo vesicles, which is essential to the overall transport efficiency of cargo vesicles. To quantitatively understand the role of the regulatory protein, we review the in vivo physical parameters of UNC-104-mediated SVP transport, including force, velocity, run length and run time, derived from wild-type and arl-8-deletion mutant C. elegans. Our future aim is to facilitate the construction of a consensus physical model to connect SVP transport with pathologies related to deficient synapse construction caused by the deficient UNC-104 regulation. We hope that the physical parameters of SVP transport summarized in this review become a useful guide for the development of such model.

physics.bio-ph↗

arXiv2018

Investigation of multiple-dynein transport of melanosomes by non-invasive force measurement using fluctuation unit $χ$

Pigment organelles known as melanosomes disperse or aggregate in a melanophore in response to hormones. These movements are mediated by the microtubule motors kinesin-2 and cytoplasmic dynein. However, the force generation mechanism of dynein, unlike that of kinesin, is not well understood. In this study, to address this issue, we investigated the dynein-mediated aggregation of melanosomes in zebrafish melanophores. We applied the fluctuation theorem of non-equilibrium statistical mechanics to estimate forces acting on melanosomes during transport by dynein, given that the energy of a system is related to its fluctuation. Our results demonstrate that multiple force-producing units cooperatively transport a single melanosome. Since the force is generated by dynein, this suggests that multiple dyneins carry a single melanosome. Cooperative transport has been reported for other organelles; thus, multiple-motor transport may be a universal mechanism for moving organelles within the cell.

physics.bio-ph↗

arXiv2018

Application of the fluctuation theorem to motor proteins: from F1-ATPase to axonal cargo transport by kinesin and dynein

The fluctuation theorem is a representative theorem in non-equilibrium statistical physics actively studied in the 1990's. Relating to entropy production in non-equilibrium states, the theorem has been used to estimate the driving power of motor proteins from fluctuation in their motion. In this review, usage of the fluctuation theorem in experiments on motor proteins is illustrated for biologists, especially those who study mechanobiology, in which force measurement is a central issue. We first introduce the application of the fluctuation theorem in measuring the rotary torque of the rotary motor protein F1-ATPase. Next, as an extension of this application, a recent trial estimating the force generated during cargo transport in vivo by the microtubule motors kinesin and dynein is introduced. Elucidation of the physical mechanism of such transport is important, especially for neurons, in which deficits in cargo transport are deeply related to neuronal diseases. Finally, perspectives on the fluctuation theorem as a new technique in the field of neuroscience are discussed.

physics.bio-ph↗

arXiv2018

Non-invasive force measurement reveals the number of active kinesins on a synaptic vesicle precursor in axonal transport regulated by ARL-8

Kinesin superfamily protein UNC-104, a member of the kinesin-3 family, transports synaptic vesicle precursors (SVPs). In this study, the number of active UNC-104 molecules hauling a single SVP in axons in the worm Caenorhabditis elegans was counted by applying a newly developed non-invasive force measurement technique. The distribution of the force acting on a SVP transported by UNC-104 was spread out over several clusters, implying the presence of several force-producing units (FPUs). We then compared the number of FPUs in the wild-type worms with that in arl-8 gene-deletion mutant worms. ARL-8 is a SVP-bound arf-like small guanosine triphosphatase, and is known to promote unlocking of the autoinhibition of the motor, which is critical for avoiding unnecessary consumption of adenosine triphosphate when the motor does not bind to a SVP. There were fewer FPUs in the arl-8 mutant worms. This finding indicates that a lack of ARL-8 decreased the number of active UNC-104 motors, which then led to a decrease in the number of motors responsible for SVP transport.

physics.bio-ph↗

arXiv2009

Rocking ratchet based on F1-ATPase in the absence of ATP

Bartussek, Hanggi and Kissner studied a rocking ratchet system, in which a Brownian particle is subject to an asymmetric periodic potential together with an oscillating force, and found that the direction of the macroscopic current can be reversed by changing the parameter values characterizing the model [Europhys. Lett., 28 (1994) 459]. In this letter, we apply their ratchet theory to a rotary motor-protein, F1-ATPase. In this work, we construct a model of a rocking ratchet in which F1-ATPase rotates not as a result of ATP hydrolysis but through the influence of an oscillating force. We then study the motion of F1-ATPase on the basis of molecular dynamics simulations of this coarse-grained protein model. Although in the absence of ATP, F1-ATPase exhibits directionless Brownian motion when there exists no oscillating force, we observe directional motion when we do apply an oscillating force. Furthermore, we observe that the direction of rotation is reversed when we change the oscillation frequency.

cond-mat.soft↗

arXiv2007

Temperature of a Hamiltonian system given as the effective temperature of a non-equilibrium steady state Langevin thermostat

In non-equilibrium steady states (NESS) far from equilibrium, it is known that the Einstein relation is violated. Then, the ratio of the diffusion coefficient to the mobility is called an effective temperature, and the physical relevance of this effective temperature has been studied in several works. Although the physical relevance is not yet completely clear, it has been found that the role of an effective temperature in NESS is indeed analogous to that of the temperature in equilibrium systems in a number of respects. In this paper, we find further evidence establishing this analogy. We employ a non-equilibrium Langevin system as a thermostat for a Hamiltonian system and find that the kinetic temperature of this Hamiltonian system is equal to the effective temperature of the thermostat.

cond-mat.stat-mech↗

arXiv2007

Fluctuation theorem applied to Dictyostelium discoideum system

In this paper, we analyze the electrotactic movement of Dictyostelium discoideum from the viewpoint of non-equilibrium statistical mechanics. Because we can observe fluctuating behavior of cellular trajectories, we analyze the probability distribution of the trajectories with the aid of the fluctuation theorem. Recently, the validity of the fluctuation theorem was verified in a colloidal system, and it has also been applied to granular systems, turbulent systems and chemical oscillatory waves to investigate some of their statistical properties that are not yet completely understood. Noting that the fluctuation theorem is potentially applicable to cellular electrotaxis, here we employ it to help us obtain a phenomenological model of this biological system.

q-bio.CB↗

arXiv2007

Violation of the fluctuation-dissipation theorem in a protein system

We report the results of molecular dynamics simulations of the protein myosin carried out with an elastic network model. Quenching the system, we observe glassy behavior of a density correlation function and a density response function that are often investigated in structure glasses and spin glasses. In the equilibrium, the fluctuation-response relation, a representative relation of the fluctuation-dissipation theorem, holds that the ratio of the density correlation function to the density response function is equal to the temperature of the environment. We show that in the quenched system that we study, this relation can be violated. In the case that this relation does not hold, this ratio can be regarded as an effective temperature. We find that this effective temperature of myosin is higher than the temperature of the environment. We discuss the relation between this effective temperature and energy transduction that occurs after ATP hydrolysis in the myosin molecule.

cond-mat.stat-mech↗

arXiv2006

Linear response theory in stochastic many-body systems revisited

The Green-Kubo relation, the Einstein relation, and the fluctuation-response relation are representative universal relations among measurable quantities that are valid in the linear response regime. We provide pedagogical proofs of these universal relations for stochastic many-body systems. Through these simple proofs, we characterize the three relations as follows. The Green-Kubo relation is a direct result of the local detailed balance condition, the fluctuation-response relation represents the dynamic extension of both the Green-Kubo relation and the fluctuation relation in equilibrium statistical mechanics, and the Einstein relation can be understood by considering thermodynamics. We also clarify the interrelationships among the universal relations.

cond-mat.stat-mech↗

arXiv2006

Computation of the Kolmogorov-Sinai entropy using statistitical mechanics: Application of an exchange Monte Carlo method

We propose a method for computing the Kolmogorov-Sinai (KS) entropy of chaotic systems. In this method, the KS entropy is expressed as a statistical average over the canonical ensemble for a Hamiltonian with many ground states. This Hamiltonian is constructed directly from an evolution equation that exhibits chaotic dynamics. As an example, we compute the KS entropy for a chaotic repeller by evaluating the thermodynamic entropy of a system with many ground states.

cond-mat.stat-mech↗

arXiv2006

The law of action and reaction for the effective force in a nonequilibrium colloidal system

We study a nonequilibrium Langevin many-body system containing two 'test' particles and many 'background' particles. The test particles are spatially confined by a harmonic potential, and the background particles are driven by an external driving force. Employing numerical simulations of the model, we formulate an effective description of the two test particles in a nonequilibrium steady state. In particular, we investigate several different definitions of the effective force acting between the test particles. We find that the law of action and reaction does not hold for the total mechanical force exerted by the background particles, but that it does hold for the thermodynamic force defined operationally on the basis of an idea used to extend the first law of thermodynamics to nonequilibrium steady states.

cond-mat.stat-mech↗

arXiv2005

Fluctuation-dissipation relations outside the linear response regime in a two-dimensional driven lattice gas along the direction transverse to the driving force

We performed numerical experiments on a two-dimensional driven lattice gas, which constitutes a simple stochastic nonequilibrium many-body model. In this model, focusing on the behavior along the direction transverse to the external driving force, we numerically measure transport coefficients and dynamical fluctuations outside the linear response regime far from equilibrium. Using these quantities, we find the validity of the Einstein relation, the Green-Kubo relation and the fluctuation-response relation.

cond-mat.stat-mech↗

arXiv2005

Exact transformation of a Langevin equation to a fluctuating response equation

We demonstrate that a Langevin equation that describes the motion of a Brownian particle under non-equilibrium conditions can be exactly transformed to a special equation that explicitly exhibits the response of the velocity to a time dependent perturbation. This transformation is constructed on the basis of an operator formulation originally used in nonlinear perturbation theory for differential equations by extending it to stochastic analysis. We find that the obtained expression is useful for the calculation of fundamental quantities of the system, and that it provides a physical basis for the decomposition of the forces in the Langevin description into effective driving, dissipative, and random forces in a large-scale description.

cond-mat.stat-mech↗

arXiv2005

Extended Einstein relations with a complex effective temperature in a one dimensional driven lattice gas

We carried out numerical experiments on a one-dimensional driven lattice gas to elucidate the statistical properties of steady states far from equilibrium. By measuring the bulk density diffusion constant $D$, the conductivity $σ$, the intensity of density fluctuations $χ$, we confirm that the Einstein relation $Dχ=σT$, which is valid in the linear response regime about equilibrium, does not hold in such steady states. Here, $T$ is the environment temperature, and the Boltzmann constant is set to unity. Recalling that the Einstein relation provided the first step in the construction of linear response theory, we attempt to extend it to a generalized form valid in steady states far from equilibrium. In order to obtain new relations among measurable quantities, we define a complex effective temperature $Θ-iΦ$ from studying the static response of the system to a slowly varying potential in space. Replacing $T$ in the Einstein relation by the real part of the effective temperature $Θ$, we numerically confirm that the relation $Dχ=σΘ$ holds in the nonequilibrium steady states far from equilibrium that we study. In addition to this extended form, we find the new relation $(L/2π)cχ=σΦ$, where $c$ represents the propagation velocity of density fluctuations.

cond-mat.stat-mech↗

arXiv2004

Decomposition of force fluctuations far from equilibrium

By studying a nonequilibrium Langevin system, we find that a simple condition determines the decomposition of the coarse-grained force into a dissipative force, an effective driving force and noise. From this condition, we derive a new universal inequality, $D \ge γ\mud^2 T$, relating the diffusion constant $D$, the differential mobility $\mud$, the bare friction constant $γ$ and the temperature $T$. Due to the general nature of the argument we present, we believe that our idea concerning this decomposition can be applied to a wide class of systems far from equilibrium.

cond-mat.stat-mech↗

arXiv2004

Effective temperature in nonequilibrium steady states of Langevin systems with a tilted periodic potential

We theoretically study Langevin systems with a tilted periodic potential. It has been known that the ratio $Θ$ of the diffusion constant to the differential mobility is not equal to the temperature of the environment (multiplied by the Boltzmann constant), except in the linear response regime, where the fluctuation dissipation theorem holds. In order to elucidate the physical meaning of $Θ$ far from equilibrium, we analyze a modulated system with a slowly varying potential. We derive a large scale description of the probability density for the modulated system by use of a perturbation method. The expressions we obtain show that $Θ$ plays the role of the temperature in the large scale description of the system and that $Θ$ can be determined directly in experiments, without measurements of the diffusion constant and the differential mobility.

cond-mat.stat-mech↗

arXiv2003

Thermodynamic relations in a driven lattice gas: numerical exprements

We explore thermodynamic relations in non-equilibrium steady states with numerical experiments on a driven lattice gas. After operationally defining the pressure and chemical potential in the driven lattice gas, we confirm numerically the validity of the integrability condition (the Maxwell relation) for the two quantities whose values differ from those for an equilibrium system. This implies that a free energy function can be constructed for the non-equilibrium steady state that we consider. We also investigate a fluctuation relation associated with this free energy function. Our result suggests that the compressibility can be expressed in terms of density fluctuations even in non-equilibrium steady states.

cond-mat.stat-mech↗