arXiv subjects

Jae-Hyung Jeon

Publications and source records attributed to Jae-Hyung Jeon.

30 records · Page 2Linked to original sources

arXiv2021

Bayesian inference of Lévy walks via hidden Markov models

The Lévy walk is a non-Brownian random walk model that has been found to describe anomalous dynamic phenomena in diverse fields ranging from biology over quantum physics to ecology. Recurrently occurring problems are to examine whether observed data are successfully quantified by a model classified as Lévy walks or not and extract the best model parameters in accordance with the data. Motivated by such needs, we propose a hidden Markov model for Lévy walks and computationally realize and test the corresponding Bayesian inference method. We introduce a Markovian decomposition scheme to approximate a renewal process governed by a power-law waiting time distribution. Using this, we construct the likelihood function of Lévy walks based on a hidden Markov model and the forward algorithm. With the Lévy walk trajectories simulated at various conditions, we perform the Bayesian inference for parameter estimation and model classification. We show that the power-law exponent of the flight-time distribution can be successfully extracted even at the condition that the mean-squared displacement does not display the expected scaling exponent due to the noise or insufficient trajectory length. It is also demonstrated that the Bayesian method performs remarkably inferring the Lévy walk trajectories from given unclassified trajectory data set if the noise level is moderate.

physics.bio-ph↗

arXiv2020

A mini-review of the diffusion dynamics of DNA-binding proteins: Experiments and models

In the course of various biological processes, specific DNA-binding proteins must find a particular target sequence/protein or a damaged site on the DNA efficiently. DNA-binding proteins perform this task based on diffusion. Yet, investigations over recent decades have found that the diffusion dynamics of DNA-binding proteins are generally complicated and, further, protein-specific. In this review, we collect the experimental and theoretical studies that quantify the diffusion dynamics of DNA-binding proteins and review them from the viewpoint of diffusion processes.

physics.bio-ph↗

arXiv2020

Anomalous diffusion for active Brownian particles cross-linked to a networked polymer: Langevin dynamics simulation and theory

Quantitatively understanding of the dynamics of an active Brownian particle (ABP) interacting with a viscoelastic polymer environment is a scientific challenge. It is intimately related to several interdisciplinary topics such as the microrheology of active colloids in a polymer matrix and the athermal dynamics of the in vivo chromosome or cytoskeletal networks. Based on Langevin dynamics simulation and analytic theory, here we explore such a viscoelastic active system in depth using a star polymer of functionality $f$ with the center cross-linker particle being ABP. We observe that the ABP cross-linker, despite its self-propelled movement, attains an active subdiffusion with the scaling $\langleΔ\mathbf{R}^2(t)\rangle\sim t^α$ with $α\leq 1/2$, through the viscoelastic feedback from the polymer. Counter-intuitively, the apparent anomaly exponent $α$ becomes smaller as the ABP is driven by a larger propulsion velocity, but is independent of the functionality $f$ or the boundary conditions of the polymer. We set forth an exact theory, and show that the motion of the active cross-linker is a gaussian non-Markovian process characterized by two distinct power-law displacement correlations. At a moderate P{é}clet number, it seemingly behaves as fractional Brownian motion with a Hurst exponent $H=α/2$, whereas, at a high P{é}clet number, the self-propelled noise in the polymer environment leads to a logarithmic growth of the mean squared displacement ($\sim \ln t$) and a velocity autocorrelation decaying as $-t^{-2}$. We demonstrate that the anomalous diffusion of the active cross-linker is precisely described by a fractional Langevin equation with two distinct random noises.

cond-mat.stat-mech↗

arXiv2019

Mapping the spectrum of 3D communities in human chromosome conformation capture data

Several experiments show that the three dimensional (3D) organization of chromosomes affects genetic processes such as transcription and gene regulation. To better understand this connection, researchers developed the Hi-C method that is able to detect the pairwise physical contacts of all chromosomal loci. The Hi-C data show that chromosomes are composed of 3D compartments that range over a variety of scales. However, it is challenging to systematically detect these cross-scale structures. Most studies have therefore designed methods for specific scales to study foremost topologically associated domains (TADs) and A/B compartments. To go beyond this limitation, we tailor a network community detection method that finds communities in compact fractal globule polymer systems. Our method allows us to continuously scan through all scales with a single resolution parameter. We found: (i) polymer segments belonging to the same 3D community do not have to be in consecutive order along the polymer chain. In other words, several TADs may belong to the same 3D community. (ii) CTCF proteins---a loop-stabilizing protein that is ascribed a big role in TAD formation---are well correlated with community borders only at one level of organization. (iii) TADs and A/B compartments are traditionally treated as two weakly related 3D structures and detected with different algorithms. With our method, we detect both by simply adjusting the resolution parameter. We therefore argue that they represent two specific levels of a continuous spectrum 3D communities, rather than seeing them as different structural entities.

q-bio.GN↗

arXiv2013

First passage behaviour of multi-dimensional fractional Brownian motion and application to reaction phenomena

Fractional Brownian motion is a generalised Gaussian diffusive process that is found to describe numerous stochastic phenomena in physics and biology. Here we introduce a multi-dimensional fractional Brownian motion (FBM) defined as a superposition of conventional FBM for each coordinate in analogy to multi-dimensional Brownian motion, and study its first passage properties. Starting from the well-established first passage time statistics of one-dimensional FBM and the associated approximation schemes, we explore the first passage time behaviour of multi-dimensional FBM and compare these results with simulations. The asymptotic kinetic behaviour of diffusion-limited reactions of reactant particles performing FBM in a one- and multi-dimensional space is studied based on the corresponding first passage time statistics.

cond-mat.stat-mech↗

arXiv2013

Noisy continuous time random walks

Experimental studies of the diffusion of biomolecules in the environment of biological cells are routinely confronted with multiple sources of stochasticity, whose identification renders the detailed data analysis of single molecule trajectories quite intricate. Here we consider subdiffusive continuous time random walks, that represent a seminal model for the anomalous diffusion of tracer particles in complex environments. This motion is characterized by multiple trapping events with infinite mean sojourn time. In real physical situations, however, instead of the full immobilization predicted by the continuous time random walk model, the motion of the tracer particle shows additional jiggling, for instance, due to thermal agitation of the environment. We here present and analyze in detail an extension of the continuous time random walk model. Superimposing the multiple trapping behavior with additive Gaussian noise of variable strength, we demonstrate that the resulting process exhibits a rich variety of apparent dynamic regimes. In particular, such noisy continuous time random walks may appear ergodic while the naked continuous time random walk exhibits weak ergodicity breaking. Detailed knowledge of this behavior will be useful for the truthful physical analysis of experimentally observed subdiffusion.

cond-mat.stat-mech↗

arXiv2012

Anomalous diffusion of phospholipids and cholesterols in a lipid bilayer and its origins

Combining extensive molecular dynamics simulations of lipid bilayer systems of varying chemical composition with single-trajectory analyses we systematically elucidate the stochastic nature of the lipid motion. We observe subdiffusion over more than four orders of magnitude in time, clearly stretching into the sub-microsecond domain. The lipid motion delicately depends on the lipid chemistry, the lipid phase, and especially on the presence of cholesterol. We demonstrate that fractional Langevin equation motion universally describes the lipid motion in all phases including the gel phase, and in the presence of cholesterol. The results underline the relevance of anomalous diffusion in lipid bilayers and the strong effects of the membrane composition.

cond-mat.soft↗

arXiv2012

Inequivalence of time and ensemble averages in ergodic systems: exponential versus power-law relaxation in confinement

Single particle tracking has become a standard tool to investigate diffusive properties, especially in small systems such as biological cells. Usually the resulting time series are analyzed in terms of time averages over individual trajectories. Here we study confined normal as well as anomalous diffusion modeled by fractional Brownian motion and the fractional Langevin equation, and show that even for such ergodic systems time-averaged quantities behave differently from their ensemble averaged counterparts, irrespective of how long the measurement time becomes. Knowledge of the exact behavior of time averages is therefore fundamental for the proper physical interpretation of measured time series, in particular, for extraction of the relaxation time scale from data.

cond-mat.stat-mech↗

arXiv2011

In vivo anomalous diffusion and weak ergodicity breaking of lipid granules

Combining extensive single particle tracking microscopy data of endogenous lipid granules in living fission yeast cells with analytical results we show evidence for anomalous diffusion and weak ergodicity breaking. Namely we demonstrate that at short times the granules perform subdiffusion according to the laws of continuous time random walk theory. The associated violation of ergodicity leads to a characteristic turnover between two scaling regimes of the time averaged mean squared displacement. At longer times the granule motion is consistent with fractional Brownian motion.

cond-mat.stat-mech↗

arXiv2010

Single particle tracking in systems showing anomalous diffusion: the role of weak ergodicity breaking

Anomalous diffusion has been widely observed by single particle tracking microscopy in complex systems such as biological cells. The resulting time series are usually evaluated in terms of time averages. Often anomalous diffusion is connected with non-ergodic behaviour. In such cases the time averages remain random variables and hence irreproducible. Here we present a detailed analysis of the time averaged mean squared displacement for systems governed by anomalous diffusion, considering both unconfined and restricted (corralled) motion. We discuss the behaviour of the time averaged mean squared displacement for two prominent stochastic processes, namely, continuous time random walks and fractional Brownian motion. We also study the distribution of the time averaged mean squared displacement around its ensemble mean, and show that this distribution preserves typical process characteristic even for short time series. Recently, velocity correlation functions were suggested to distinguish between these processes. We here present analytucal expressions for the velocity correlation functions. Knowledge of the results presented here are expected to be relevant for the correct interpretation of single particle trajectory data in complex systems.

cond-mat.stat-mech↗

arXiv2010

How dsDNA breathing enhances its flexibility and instability on short length scales

We study the unexpected high flexibility of short dsDNA which recently has been reported by a number of experiments. Via the Langevin dynamics simulation of our Breathing DNA model, first we observe the formation of bubbles within the duplex and also forks at the ends, with the size distributions independent of the contour length. We find that these local denaturations at a physiological temperature, despite their rare and transient presence, can lower the persistence length drastically for a short DNA segment in agreement with experiment.

cond-mat.soft↗

arXiv2010

Fractional Brownian motion and generalized Langevin equation motion in confined geometries

Motivated by subdiffusive motion of bio-molecules observed in living cells we study the stochastic properties of a non-Brownian particle whose motion is governed by either fractional Brownian motion or the fractional Langevin equation and restricted to a finite domain. We investigate by analytic calculations and simulations how time-averaged observables (e.g., the time averaged mean squared displacement and displacement correlation) are affected by spatial confinement and dimensionality. In particular we study the degree of weak ergodicity breaking and scatter between different single trajectories for this confined motion in the subdiffusive domain. The general trend is that deviations from ergodicity are decreased with decreasing size of the movement volume, and with increasing dimensionality. We define the displacement correlation function and find that this quantity shows distinct features for fractional Brownian motion, fractional Langevin equation, and continuous time subdiffusion, such that it appears an efficient measure to distinguish these different processes based on single particle trajectory data.

cond-mat.stat-mech↗