@article{MetzlerJeon2012, author = {Metzler, Ralf and Jeon, Jae-Hyung}, title = {The role of ergodicity in anomalous stochastic processes - analysis of single-particle trajectories}, series = {Physica scripta : an international journal for experimental and theoretical physics}, volume = {86}, journal = {Physica scripta : an international journal for experimental and theoretical physics}, number = {5}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {0031-8949}, doi = {10.1088/0031-8949/86/05/058510}, pages = {5}, year = {2012}, abstract = {Single-particle experiments produce time series x(t) of individual particle trajectories, frequently revealing anomalous diffusion behaviour. Typically, individual x(t) are evaluated in terms of time-averaged quantities instead of ensemble averages. Here we discuss the behaviour of the time-averaged mean squared displacement of different stochastic processes giving rise to anomalous diffusion. In particular, we pay attention to the ergodic properties of these processes, i.e. the (non)equivalence of time and ensemble averages.}, language = {en} } @article{RevereyJeonBaoetal.2015, author = {Reverey, Julia F. and Jeon, Jae-Hyung and Bao, Han and Leippe, Matthias and Metzler, Ralf and Selhuber-Unkel, Christine}, title = {Superdiffusion dominates intracellular particle motion in the supercrowded cytoplasm of pathogenic Acanthamoeba castellanii}, series = {Scientific reports}, volume = {5}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep11690}, pages = {14}, year = {2015}, abstract = {Acanthamoebae are free-living protists and human pathogens, whose cellular functions and pathogenicity strongly depend on the transport of intracellular vesicles and granules through the cytosol. Using high-speed live cell imaging in combination with single-particle tracking analysis, we show here that the motion of endogenous intracellular particles in the size range from a few hundred nanometers to several micrometers in Acanthamoeba castellanii is strongly superdiffusive and influenced by cell locomotion, cytoskeletal elements, and myosin II. We demonstrate that cell locomotion significantly contributes to intracellular particle motion, but is clearly not the only origin of superdiffusivity. By analyzing the contribution of microtubules, actin, and myosin II motors we show that myosin II is a major driving force of intracellular motion in A. castellanii. The cytoplasm of A. castellanii is supercrowded with intracellular vesicles and granules, such that significant intracellular motion can only be achieved by actively driven motion, while purely thermally driven diffusion is negligible.}, language = {en} } @article{JeonChechkinMetzler2014, author = {Jeon, Jae-Hyung and Chechkin, Aleksei V. and Metzler, Ralf}, title = {Scaled Brownian motion: a paradoxical process with a time dependent diffusivity for the description of anomalous diffusion}, series = {Physical chemistry, chemical physics : PCCP}, volume = {30}, journal = {Physical chemistry, chemical physics : PCCP}, number = {16}, publisher = {The Royal Society of Chemistry}, address = {Cambridge}, doi = {10.1039/C4CP02019G}, pages = {15811 -- 15817}, year = {2014}, abstract = {Anomalous diffusion is frequently described by scaled Brownian motion (SBM){,} a Gaussian process with a power-law time dependent diffusion coefficient. Its mean squared displacement is ?x2(t)? [similar{,} equals] 2K(t)t with K(t) [similar{,} equals] t[small alpha]-1 for 0 < [small alpha] < 2. SBM may provide a seemingly adequate description in the case of unbounded diffusion{,} for which its probability density function coincides with that of fractional Brownian motion. Here we show that free SBM is weakly non-ergodic but does not exhibit a significant amplitude scatter of the time averaged mean squared displacement. More severely{,} we demonstrate that under confinement{,} the dynamics encoded by SBM is fundamentally different from both fractional Brownian motion and continuous time random walks. SBM is highly non-stationary and cannot provide a physical description for particles in a thermalised stationary system. Our findings have direct impact on the modelling of single particle tracking experiments{,} in particular{,} under confinement inside cellular compartments or when optical tweezers tracking methods are used.}, language = {en} } @article{JeonChechkinMetzler2014, author = {Jeon, Jae-Hyung and Chechkin, Aleksei V. and Metzler, Ralf}, title = {Scaled Brownian motion: a paradoxical process with a time dependent diffusivity for the description of anomalous diffusion}, series = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, volume = {16}, journal = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, number = {30}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9076}, doi = {10.1039/c4cp02019g}, pages = {15811 -- 15817}, year = {2014}, abstract = {Anomalous diffusion is frequently described by scaled Brownian motion (SBM), a Gaussian process with a power-law time dependent diffusion coefficient. Its mean squared displacement is < x(2)(t) similar or equal to 2K(t)t with K(t) similar or equal to t(alpha-1) for 0 < alpha < 2. SBM may provide a seemingly adequate description in the case of unbounded diffusion, for which its probability density function coincides with that of fractional Brownian motion. Here we show that free SBM is weakly non-ergodic but does not exhibit a significant amplitude scatter of the time averaged mean squared displacement. More severely, we demonstrate that under confinement, the dynamics encoded by SBM is fundamentally different from both fractional Brownian motion and continuous time random walks. SBM is highly non-stationary and cannot provide a physical description for particles in a thermalised stationary system. Our findings have direct impact on the modelling of single particle tracking experiments, in particular, under confinement inside cellular compartments or when optical tweezers tracking methods are used.}, language = {en} } @misc{JeonChechkinMetzler2014, author = {Jeon, Jae-Hyung and Chechkin, Aleksei V. and Metzler, Ralf}, title = {Scaled Brownian motion: a paradoxical process with a time dependent diffusivity for the description of anomalous diffusion}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-76302}, pages = {15811 -- 15817}, year = {2014}, abstract = {Anomalous diffusion is frequently described by scaled Brownian motion (SBM){,} a Gaussian process with a power-law time dependent diffusion coefficient. Its mean squared displacement is ?x2(t)? [similar{,} equals] 2K(t)t with K(t) [similar{,} equals] t[small alpha]-1 for 0 < [small alpha] < 2. SBM may provide a seemingly adequate description in the case of unbounded diffusion{,} for which its probability density function coincides with that of fractional Brownian motion. Here we show that free SBM is weakly non-ergodic but does not exhibit a significant amplitude scatter of the time averaged mean squared displacement. More severely{,} we demonstrate that under confinement{,} the dynamics encoded by SBM is fundamentally different from both fractional Brownian motion and continuous time random walks. SBM is highly non-stationary and cannot provide a physical description for particles in a thermalised stationary system. Our findings have direct impact on the modelling of single particle tracking experiments{,} in particular{,} under confinement inside cellular compartments or when optical tweezers tracking methods are used.}, language = {en} } @article{AdamcikJeonKarczewskietal.2012, author = {Adamcik, Jozef and Jeon, Jae-Hyung and Karczewski, Konrad J. and Metzler, Ralf and Dietler, Giovanni}, title = {Quantifying supercoiling-induced denaturation bubbles in DNA}, series = {Soft matter}, volume = {8}, journal = {Soft matter}, number = {33}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1744-683X}, doi = {10.1039/c2sm26089a}, pages = {8651 -- 8658}, year = {2012}, abstract = {In both eukaryotic and prokaryotic DNA sequences of 30-100 base-pairs rich in AT base-pairs have been identified at which the double helix preferentially unwinds. Such DNA unwinding elements are commonly associated with origins for DNA replication and transcription, and with chromosomal matrix attachment regions. Here we present a quantitative study of local DNA unwinding based on extensive single DNA plasmid imaging. We demonstrate that long-lived single-stranded denaturation bubbles exist in negatively supercoiled DNA, at the expense of partial twist release. Remarkably, we observe a linear relation between the degree of supercoiling and the bubble size, in excellent agreement with statistical modelling. Furthermore, we obtain the full distribution of bubble sizes and the opening probabilities at varying salt and temperature conditions. The results presented herein underline the important role of denaturation bubbles in negatively supercoiled DNA for biological processes such as transcription and replication initiation in vivo.}, language = {en} } @article{JeonJavanainenMartinezSearaetal.2016, author = {Jeon, Jae-Hyung and Javanainen, Matti and Martinez-Seara, Hector and Metzler, Ralf and Vattulainen, Ilpo}, title = {Protein Crowding in Lipid Bilayers Gives Rise to Non-Gaussian Anomalous Lateral Diffusion of Phospholipids and Proteins}, series = {Physical review : X, Expanding access}, volume = {6}, journal = {Physical review : X, Expanding access}, publisher = {American Physical Society}, address = {College Park}, issn = {2160-3308}, doi = {10.1103/PhysRevX.6.021006}, pages = {17}, year = {2016}, abstract = {Biomembranes are exceptionally crowded with proteins with typical protein-to-lipid ratios being around 1:50 - 1:100. Protein crowding has a decisive role in lateral membrane dynamics as shown by recent experimental and computational studies that have reported anomalous lateral diffusion of phospholipids and membrane proteins in crowded lipid membranes. Based on extensive simulations and stochastic modeling of the simulated trajectories, we here investigate in detail how increasing crowding by membrane proteins reshapes the stochastic characteristics of the anomalous lateral diffusion in lipid membranes. We observe that correlated Gaussian processes of the fractional Langevin equation type, identified as the stochastic mechanism behind lipid motion in noncrowded bilayer, no longer adequately describe the lipid and protein motion in crowded but otherwise identical membranes. It turns out that protein crowding gives rise to a multifractal, non-Gaussian, and spatiotemporally heterogeneous anomalous lateral diffusion on time scales from nanoseconds to, at least, tens of microseconds. Our investigation strongly suggests that the macromolecular complexity and spatiotemporal membrane heterogeneity in cellular membranes play critical roles in determining the stochastic nature of the lateral diffusion and, consequently, the associated dynamic phenomena within membranes. Clarifying the exact stochastic mechanism for various kinds of biological membranes is an important step towards a quantitative understanding of numerous intramembrane dynamic phenomena.}, language = {en} } @article{JeonBarkaiMetzler2013, author = {Jeon, Jae-Hyung and Barkai, Eli and Metzler, Ralf}, title = {Noisy continuous time random walks}, series = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr}, volume = {139}, journal = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr}, number = {12}, publisher = {American Institute of Physics}, address = {Melville}, issn = {0021-9606}, doi = {10.1063/1.4816635}, pages = {15}, year = {2013}, abstract = {Experimental studies of the diffusion of biomolecules within 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 bare 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.}, language = {en} } @article{JeonMetzler2012, author = {Jeon, Jae-Hyung and Metzler, Ralf}, title = {Inequivalence of time and ensemble averages in ergodic systems: exponential versus power-law relaxation in confinement}, series = {Physical review : E, Statistical, nonlinear and soft matter physics}, volume = {85}, journal = {Physical review : E, Statistical, nonlinear and soft matter physics}, number = {2}, publisher = {American Physical Society}, address = {College Park}, issn = {1539-3755}, doi = {10.1103/PhysRevE.85.021147}, pages = {8}, year = {2012}, abstract = {Single-particle tracking has become a standard tool for the investigation of 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.}, language = {en} } @article{MardoukhiJeonMetzler2015, author = {Mardoukhi, Yousof and Jeon, Jae-Hyung and Metzler, Ralf}, title = {Geometry controlled anomalous diffusion in random fractal geometries: looking beyond the infinite cluster}, series = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, volume = {17}, journal = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, number = {44}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9076}, doi = {10.1039/c5cp03548a}, pages = {30134 -- 30147}, year = {2015}, abstract = {We investigate the ergodic properties of a random walker performing (anomalous) diffusion on a random fractal geometry. Extensive Monte Carlo simulations of the motion of tracer particles on an ensemble of realisations of percolation clusters are performed for a wide range of percolation densities. Single trajectories of the tracer motion are analysed to quantify the time averaged mean squared displacement (MSD) and to compare this with the ensemble averaged MSD of the particle motion. Other complementary physical observables associated with ergodicity are studied, as well. It turns out that the time averaged MSD of individual realisations exhibits non-vanishing fluctuations even in the limit of very long observation times as the percolation density approaches the critical value. This apparent non-ergodic behaviour concurs with the ergodic behaviour on the ensemble averaged level. We demonstrate how the non-vanishing fluctuations in single particle trajectories are analytically expressed in terms of the fractal dimension and the cluster size distribution of the random geometry, thus being of purely geometrical origin. Moreover, we reveal that the convergence scaling law to ergodicity, which is known to be inversely proportional to the observation time T for ergodic diffusion processes, follows a power-law similar to T-h with h < 1 due to the fractal structure of the accessible space. These results provide useful measures for differentiating the subdiffusion on random fractals from an otherwise closely related process, namely, fractional Brownian motion. Implications of our results on the analysis of single particle tracking experiments are provided.}, language = {en} }