arXiv subjects

Yuichi Itto

Publications and source records attributed to Yuichi Itto.

17 recordsLinked to original sources

arXiv2025

On the thermodynamic analogy of intracellular diffusivity fluctuations

Two recent topics on a formal thermodynamic analogy of intracellular diffusivity fluctuations observed experimentally in normal/anomalous diffusion are reported. Not only the analogs of the quantity of heat and work as well as the internal energy but also that of the Clausius inequality are identified. Then, the analog of the heat engine is constructed to characterize extraction of the diffusivity change as the analog of work during a cycle, the efficiency of which is formally equivalent to that of the Carnot engine, making the total change of the entropy concerning the fluctuations vanish. The effect of the slow variation of the fluctuations on the efficiency is also briefly discussed.

cond-mat.stat-mech↗

arXiv2025

Analog of the Carnot engine for fluctuating diffusivity in living cells

Recently, a formal analogy between the fluctuating diffusivity and thermodynamics has been proposed based on phenomena of heterogeneous diffusion observed in living cells. This not only offers the analogs of the quantity of heat and work as well as the internal energy but also achieves that of the Clausius inequality for the entropy concerning diffusivity fluctuations. Here, a discussion is developed about constructing a heat-like engine in terms of the fluctuating diffusivity. The engine constitutes two kinds of processes with the average diffusivity or the average local temperature being kept fixed, along which the fluctuation distribution obeys an exponential law. The efficiency of the engine in a cycle, which quantifies how much the diffusivity change as the analog of work can be extracted, is found to formally coincide with that of Carnot's. During the cycle, the total change of the entropy is also shown to vanish.

cond-mat.stat-mech↗

arXiv2023

Conditional entropy and weak fluctuation correlation in nonequilibrium complex systems

The weak correlation between spatiotemporal fluctuations in nonequilibrium complex systems is shown to govern the fluctuation distribution, maximizing the conditional entropy associated with such fluctuations. The result is illustrated in diffusion phenomena observed in living cells. A generic feature of the weak correlation is briefly mentioned.

cond-mat.stat-mech↗

arXiv2023

Conditional entropic approach to nonequilibrium complex systems with weak fluctuation correlation

A conditional entropic approach is discussed for nonequilibrium complex systems with a weak correlation between spatiotemporally fluctuating quantities on a large time scale. The weak correlation is found to constitute the fluctuation distribution that maximizes the entropy associated with the conditional fluctuations. The approach is illustrated in diffusion phenomenon of proteins inside bacteria. A further possible illustration is also presented for membraneless organelles in embryos and beads in cell extracts, which share common natures of fluctuations in their diffusion.

cond-mat.stat-mech↗

arXiv2021

Weak correlation between fluctuations in protein diffusion inside bacteria

A weak correlation between the diffusion-exponent fluctuations and the temperature fluctuations is discussed based on recent experimental observations for protein diffusion inside bacteria. Its existence is shown to be essential for describing the statistical properties of the fluctuations. It is also quantified how largely the fluctuations are modulated by the weak correlation.

cond-mat.stat-mech↗

arXiv2021

Fluctuating diffusivity of RNA-protein particles: Analogy with thermodynamics

A formal analogy of fluctuating diffusivity to thermodynamics is discussed for messenger RNA molecules fluorescently fused to a protein in living cells. Regarding the average value of the fluctuating diffusivity of such RNA-protein particles as the analog of the internal energy, the analogs of the quantity of heat and work are identified. The Clausius-like inequality is shown to hold for the entropy associated with diffusivity fluctuations, which plays a role analogous to the thermodynamic entropy, and the analog of the quantity of heat. The change of the statistical fluctuation distribution is also examined from a geometric perspective. The present discussions may contribute to a deeper understanding of the fluctuating diffusivity in view of the laws of thermodynamics.

cond-mat.stat-mech↗

arXiv2021

Superstatistical modelling of protein diffusion dynamics in bacteria

A recent experiment [Sadoon AA, Wang Y. 2018 Phys. Rev. E 98, 042411] has revealed that nucleoid associated proteins (i.e., DNA-binding proteins) exhibit highly heterogeneous diffusion processes in bacteria where not only the diffusion constant but also the anomalous diffusion exponent fluctuates for the various proteins. The distribution of displacements of such proteins is observed to take a q-Gaussian form, which decays as a power law. Here, a statistical model is developed for the diffusive motion of the proteins within the bacterium, based on a superstatistics with two variables. This model hierarchically takes into account the joint fluctuations of both the anomalous diffusion exponents and the diffusion constants. A fractional Brownian motion is discussed as a possible local model. Good agreement with the experimental data is obtained.

cond-mat.stat-mech↗

arXiv2019

Time evolution of entropy associated with diffusivity fluctuations: Diffusing diffusivity approach

It has experimentally been found by Lampo et al. [Biophys. J. 112, 532 (2017)] that, for two different types of cell, the distribution of the diffusivities of RNA-protein particles over cytoplasm obeys an exponential law. Then, an interesting issue has been pointed out: this exponential distribution is the maximal entropy distribution. Here, time evolution of entropy associated with local fluctuations of the diffusivity is studied. The entropy rate under the diffusing diffusivity equation, which admits the exponential fluctuation as its stationary solution, is shown to be positive. The present result is expected to be useful for studying the dynamics of diffusivity fluctuations. Furthermore, the distribution of time being required for characteristic displacement of the RNA-protein particle is found to decay as a power law. A comment is also made on a formal analogy with the thermodynamic relation concerning temperature.

physics.bio-ph↗

arXiv2018

Sojourn-time distribution of virus capsid in interchromatin corrals of a cell nucleus

Virus capsids in interchromatin corrals of a cell nucleus are experimentally known to exhibit anomalous diffusion as well as normal diffusion, leading to the Gaussian distribution of the diffusion-exponent fluctuations over the corrals. Here, the sojourn-time distribution of the virus capsid in local areas of the corral, i.e., probability distribution of the sojourn time characterizing diffusion in the local areas, is examined. Such an area is regarded as a virtual cubic block, the diffusion property in which is normal or anomalous. The distribution, in which the Gaussian fluctuation is incorporated, is shown to tend to slowly decay. Then, the block-size dependence of average sojourn time is discussed. A comment is also made on (non-)Markovianity of the process of moving through the blocks.

physics.bio-ph↗

arXiv2018

Gaussian fluctuation of the diffusion exponent of virus capsid in a living cell nucleus

In their work [Proc. Natl. Acad. Sci. USA 112 (2015) E5725], Bosse et al. experimentally showed that virus capsid exhibits not only normal diffusion but also anomalous diffusion in nucleus of a living cell. There, it was found that the distribution of fluctuations of the diffusion exponent characterizing them takes the Gaussian form, which is, quite remarkably, the same form for two different types of the virus. This suggests high robustness of such fluctuations. Here, the statistical property of local fluctuations of the diffusion exponent of the virus capsid in the nucleus is studied. A maximum-entropy-principle approach (originally proposed for a different virus in a different cell) is applied for obtaining the fluctuation distribution of the exponent. Largeness of the number of blocks identified with local areas of interchromatin corrals is also examined based on the experimental data. It is shown that the Gaussian distribution of the local fluctuations can be derived, in accordance with the above form. In addition, it is quantified how the fluctuation distribution on a long time scale is different from the Gaussian distribution.

physics.bio-ph↗

arXiv2018

Diffusion theory for the infection pathway of virus in a living cell

The infection pathway of virus in living cell is of interest from the viewpoint of the physics of diffusion. Here, recent developments about a diffusion theory for the infection pathway of an adeno-associated virus in cytoplasm of a living HeLa cell are reported. Generalizing fractional kinetics successfully modeling anomalous diffusion, a theory for describing the infection pathway of the virus over the cytoplasm is presented. The statistical property of the fluctuations of the anomalous-diffusion exponent is also discussed based on a maximum-entropy-principle approach. In addition, an issue regarding the continuum limit of the entropy introduced in the approach is carefully examined. The theory is found to imply that the motion of the virus may obey a scaling law.

physics.bio-ph↗

arXiv2016

Deviation of the statistical fluctuation in heterogeneous anomalous diffusion

The exponent of anomalous diffusion of virus in cytoplasm of a living cell is experimentally known to fluctuate depending on localized areas of the cytoplasm, indicating heterogeneity of diffusion. In a recent paper (Itto, 2012), a maximum-entropy-principle approach has been developed in order to propose an Ansatz for the statistical distribution of such exponent fluctuations. Based on this approach, here the deviation of the statistical distribution of the fluctuations from the proposed one is studied from the viewpoint of Einstein's theory of fluctuations (of the thermodynamic quantities). This may present a step toward understanding the statistical property of the deviation. It is shown in a certain class of small deviations that the deviation obeys the multivariate Gaussian distribution.

physics.bio-ph↗

arXiv2014

Heterogeneous anomalous diffusion in view of superstatistics

It is experimentally known that virus exhibits stochastic motion in cytoplasm of a living cell in the free form as well as the form being contained in the endosome and the exponent of anomalous diffusion of the virus fluctuates depending on localized areas of the cytoplasm. Here, a theory is developed for establishing a generalized fractional kinetics for the infection pathway of the virus in the cytoplasm in view of superstatistics, which offers a general framework for describing nonequilibrium complex systems with two largely separated time scales. In the present theory, the existence of a large time-scale separation in the infection pathway is explicitly taken into account. A comment is also made on scaling nature of the motion of the virus that is suggested by the theory.

physics.bio-ph↗

arXiv2012

On the Geodesic Nature of Wegner's Flow

Wegner's method of flow equations offers a useful tool for diagonalizing a given Hamiltonian and is widely used in various branches of quantum physics. Here, generalizing this method, a condition is derived, under which the corresponding flow of a quantum state becomes geodesic in a submanifold of the projective Hilbert space, independently of specific initial conditions. This implies the geometric optimality of the present method as an algorithm of generating stationary states. The result is illustrated by analyzing some physical examples.

quant-ph↗

arXiv2010

Heterogeneous anomalous diffusion of virus in cytoplasm of a living cell

The infection pathway of virus in cytoplasm of a living cell is studied from the viewpoint of diffusion theory. The cytoplasm plays a role of a medium for stochastic motion of the virus contained in the endosome as well as the free virus. It is experimentally known that the exponent of anomalous diffusion fluctuates in localized areas of the cytoplasm. Here, generalizing fractional kinetic theory, such fluctuations are described in terms of the exponent locally distributed over the cytoplasm, and a theoretical proposition is presented for its statistical form. The proposed fluctuations may be examined in an experiment of heterogeneous diffusion in the infection pathway.

physics.bio-ph↗

arXiv2009

Statistical quantum operation

A generic unital positive operator-valued measure (POVM), which transforms a given stationary pure state to an arbitrary statistical state with perfect decoherence, is presented. This allows one to operationally realize thermalization as a special case. The loss of information due to randomness generated by the operation is discussed by evaluating the entropy. Thermalization of the bipartite spin-1/2 system is discussed as an illustrative example.

cond-mat.stat-mech↗

arXiv2007

Stationary photon-atom entanglement and flow equation

Stationary photon-atom entanglement is discussed by applying the method of flow equation to the Jaynes-Cummings model. A nonlocal continuous unitary transformation is explicitly constructed and the associated positive operator-valued measures for the photons and atom are obtained. Then, flow of the entanglement entropy is analyzed. A comment is also made on implementing the unitary operation in the method of flow equation. This method may offer a new strategy for quantum-state engineering.

quant-ph↗