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.
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…
A generalized Langevin equation with fluctuating diffusivity (GLEFD) is proposed, and it is shown that the GLEFD satisfies a generalized fluctuation-dissipation relation. If the memory kernel is a power law, the GLEFD exhibits anomalous subdiffusion, non-Gaussianity, and stretched-exponential relaxation. The case in which the memory kernel is given by a single exponential function is also investigated as an analytically tractable example. In particular, the mean-square displacement and the self-intermediate-scattering function of this system show plateau structures. A numerical scheme to integ…
Extracting the intrinsic kinetic information of biological molecule from its single-molecule kinetic data is of considerable biophysical interest. In this work, we theoretically investigate the feasibility of inferring single RNA's intrinsic kinetic parameters from the time series obtained by forced folding/unfolding experiment done in the light tweezer, where the molecule is flanked by long double-stranded DNA/RNA handles and tethered between two big beads. We first construct a coarse-grain physical model of the experimental system. The model has captured the major physical factors: the Brown…
We consider Langevin equation with dichotomously fluctuating diffusivity, where the diffusion coefficient changes dichotomously in time, in order to study fluctuations of time-averaged observables in temporary heterogeneous diffusion process. We find that occupation time statistics is a powerful tool for calculating the time-averaged mean square displacement in the model. We show that the time-averaged diffusion coefficients are intrinsically random when the mean sojourn time for one of the states diverges. Our model provides anomalous fluctuations of time-averaged diffusivity, which have rele…
We investigate the ensemble and time averaged mean squared displacements for particle diffusion in a simple model for disordered media by assuming that the local diffusivity is both fluctuating in time and has a deterministic average growth or decay in time. In this study we compare computer simulations of the stochastic Langevin equation for this random diffusion process with analytical results. We explore the regimes of normal Brownian motion as well as anomalous diffusion in the sub- and superdiffusive regimes. We also consider effects of the inertial term on the particle motion. The invest…
Recently, anomalous subdiffusion, aging, and scatter of the diffusion coefficient have been reported in many single-particle-tracking experiments, though origins of these behaviors are still elusive. Here, as a model to describe such phenomena, we investigate a Langevin equation with diffusivity fluctuating between a fast and a slow state. We assume that the sojourn time distributions of these two states are given by power laws. It is shown that, for a non-equilibrium ensemble, the ensemble-averaged mean square displacement (MSD) shows transient subdiffusion. In contrast, the time-averaged MSD…
The mean-square displacement (MSD) is widely utilized to study the dynamical properties of stochastic processes. The time-averaged MSD (TAMSD) provides some information on the dynamics which cannot be extracted from the ensemble-averaged MSD. In particular, the relative standard deviation (RSD) of the TAMSD can be utilized to study the long time relaxation behavior. In this work, we consider a class of Langevin equations which are multiplicatively coupled to time-dependent and fluctuating diffusivities. Various interesting dynamics models such as entangled polymers and supercooled liquids can …
There have been increasing reports that the diffusion coefficient of macromolecules depends on time and fluctuates randomly. Here, a novel method to elucidate the fluctuating diffusivity from trajectory data is developed. The time-averaged mean square displacement (MSD), a common tool in single-particle-tracking (SPT) experiments, is generalized into a second order tensor, with which information on both magnitude fluctuations and orientational fluctuations of the diffusivity can be clearly detected. This new method is utilized to analyze the center-of-mass motion of four polymer models, the Ro…
We investigate Brownian motion with diffusivity alternately fluctuating between fast and slow states. We assume that sojourn-time distributions of these two states are given by exponential or power-law distributions. We develop a theory of alternating renewal processes to study a relaxation function which is expressed with an integral of the diffusivity over time. This relaxation function can be related to a position correlation function if the particle is in a harmonic potential, and to the self-intermediate scattering function if the potential force is absent. It is theoretically shown that,…
We study a relaxation behavior of an Ornstein-Uhlenbeck (OU) process with a time-dependent and fluctuating diffusivity. In this process, the dynamics of a position vector is modeled by the Langevin equation with a linear restoring force and a fluctuating diffusivity (FD). This process can be interpreted as a simple model of the relaxational dynamics with internal degrees of freedom or in a heterogeneous environment. By utilizing the functional integral expression and the transfer matrix method, we show that the relaxation function can be expressed in terms of the eigenvalues and eigenfunctions…
Dynamical random walk of classical particle in thermodynamically equilibrium fluctuating medium, - Gaussian random potential field, - is considered in the framework of explicit stochastic representation of deterministic interactions. We discuss corresponding formally exact Langevin equations for the particle's trajectory and show that Marcovian kinetic equation approximation to them is inadequate, - even (and especially) in case of spatially-temporally short-correlated field, - since ignores such actual effects of exponential instability of the trajectory (in respect to small perturbations) as…
Anomalous statistics in the Langevin equation with fluctuating diffusivity: from Brownian yet non-Gaussian diffusion to anomalous diffusion and ergodicity breaking
Tokyo University of Science（东京科学大学）；Pohang University of Science and Technology（浦项科技大学）；Asia Pacific Centre for Theoretical Physics（亚太理论物理中心）；University of Potsdam（波茨坦大学）；Wakayama University（和歌山大学）；Nagoya University（名古屋大学）；Keio University（庆应义塾大学）
In heterogeneous environments, the diffusivity is not constant but changes with time. It is important to detect changes in the diffusivity from single-particle-tracking trajectories in experiments. Here, we devise a novel method for detecting the transition times of the diffusivity from trajectory data. A key idea of this method is the introduction of a characteristic time scale of the diffusive states, which is obtained by a fluctuation analysis of the time-averaged mean square displacements. We test our method in silico by using the Langevin equation with a fluctuating diffusivity. We show t…
A considerable number of systems have recently been reported in which Brownian yet non-Gaussian dynamics was observed. These are processes characterised by a linear growth in time of the mean squared displacement, yet the probability density function of the particle displacement is distinctly non-Gaussian, and often of exponential (Laplace) shape. This apparently ubiquitous behaviour observed in very different physical systems has been interpreted as resulting from diffusion in inhomogeneous environments and mathematically represented through a variable, stochastic diffusion coefficient. Indee…
The active Brownian particle (ABP) model describes a swimmer, synthetic or living, whose direction of swimming is a Brownian motion. The swimming is due to a propulsion force, and the fluctuations are typically thermal in origin. We present a 2D model where the fluctuations arise from nonthermal noise in a propelling force acting at a single point, such as that due to a flagellum. We take the overdamped limit and find several modifications to the traditional ABP model. Since the fluctuating force causes a fluctuating torque, the diffusion tensor describing the process has a coupling between tr…
The cellular cytoplasm is organized into compartments. Phase separation is a simple manner to create membrane-less compartments in order to confine and localize particles like proteins. In many cases these particles are bound to fluctuating polymers like DNA or RNA. We propose a general theoretical framework for such polymer-bound particles and derive an effective 1D lattice gas model with both nearest-neighbor and emergent long-range interactions arising from looped configurations of the fluctuating polymer. We argue that 1D phase transitions exist in such systems for both Gaussian and self-a…
We introduce a general class of stochastic lattice gas models, and derive their fluctuating hydrodynamics description in the large size limit under a local equilibrium hypothesis. The model consists in energetic particles on a lattice subject to exclusion interactions, which move and collide stochastically with energy-dependent rates. The resulting fluctuating hydrodynamics equations exhibit nonlinear coupled particle and energy transport, including particle currents due to temperature gradients (Soret effect) and energy flow due to concentration gradients (Dufour effect). The microscopic dyna…
