TY - JOUR A1 - Cherstvy, Andrey G. A1 - Chechkin, Aleksei V. A1 - Metzler, Ralf T1 - Ageing and confinement in non-ergodic heterogeneous diffusion processes JF - Journal of physics : A, Mathematical and theoretical N2 - We study the effects of ageing-the time delay between initiation of the physical process at t = 0 and start of observation at some time t(a) > 0-and spatial confinement on the properties of heterogeneous diffusion processes (HDPs) with deterministic power-law space-dependent diffusivities, D(x) = D-0 vertical bar x vertical bar(alpha). From analysis of the ensemble and time averaged mean squared displacements and the ergodicity breaking parameter quantifying the inherent degree of irreproducibility of individual realizations of the HDP we obtain striking similarities to ageing subdiffusive continuous time random walks with scale-free waiting time distributions. We also explore how both processes can be distinguished. For confined HDPs we study the long-time saturation of the ensemble and time averaged particle displacements as well as the magnitude of the inherent scatter of time averaged displacements and contrast the outcomes to the results known for other anomalous diffusion processes under confinement. KW - stochastic processes KW - anomalous diffusion KW - ageing KW - weak ergodicity breaking Y1 - 2014 U6 - https://doi.org/10.1088/1751-8113/47/48/485002 SN - 1751-8113 SN - 1751-8121 VL - 47 IS - 48 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Metzler, Ralf A1 - Sanders, L. A1 - Lomholt, M. A. A1 - Lizana, L. A1 - Fogelmark, K. A1 - Ambjoernsson, Tobias T1 - Ageing single file motion JF - The European physical journal Y1 - 2014 U6 - https://doi.org/10.1140/epjst/e2014-02333-5 SN - 1951-6355 SN - 1951-6401 VL - 223 IS - 14 SP - 3287 EP - 3293 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Schulz, Johannes H. P. A1 - Barkai, Eli A1 - Metzler, Ralf T1 - Aging renewal theory and application to random walks JF - Physical review : X, Expanding access N2 - We discuss a renewal process in which successive events are separated by scale-free waiting time periods. Among other ubiquitous long-time properties, this process exhibits aging: events counted initially in a time interval [0, t] statistically strongly differ from those observed at later times [t(a,) t(a) + t]. The versatility of renewal theory is owed to its abstract formulation. Renewals can be interpreted as steps of a random walk, switching events in two-state models, domain crossings of a random motion, etc. In complex, disordered media, processes with scale-free waiting times play a particularly prominent role. We set up a unified analytical foundation for such anomalous dynamics by discussing in detail the distribution of the aging renewal process. We analyze its half-discrete, half-continuous nature and study its aging time evolution. These results are readily used to discuss a scale-free anomalous diffusion process, the continuous-time random walk. By this, we not only shed light on the profound origins of its characteristic features, such as weak ergodicity breaking, along the way, we also add an extended discussion on aging effects. In particular, we find that the aging behavior of time and ensemble averages is conceptually very distinct, but their time scaling is identical at high ages. Finally, we show how more complex motion models are readily constructed on the basis of aging renewal dynamics. Y1 - 2014 U6 - https://doi.org/10.1103/PhysRevX.4.011028 SN - 2160-3308 VL - 4 IS - 1 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Metzler, Ralf A1 - Jeon, Jae-Hyung A1 - Cherstvy, Andrey G. A1 - Barkai, Eli T1 - Anomalous diffusion models and their properties BT - non-stationarity, non-ergodicity, and ageing at the centenary of single particle tracking JF - physical chemistry, chemical physics : PCCP N2 - Modern microscopic techniques following the stochastic motion of labelled tracer particles have uncovered significant deviations from the laws of Brownian motion in a variety of animate and inanimate systems. Such anomalous diffusion can have different physical origins, which can be identified from careful data analysis. In particular, single particle tracking provides the entire trajectory of the traced particle, which allows one to evaluate different observables to quantify the dynamics of the system under observation. We here provide an extensive overview over different popular anomalous diffusion models and their properties. We pay special attention to their ergodic properties, highlighting the fact that in several of these models the long time averaged mean squared displacement shows a distinct disparity to the regular, ensemble averaged mean squared displacement. In these cases, data obtained from time averages cannot be interpreted by the standard theoretical results for the ensemble averages. Here we therefore provide a comparison of the main properties of the time averaged mean squared displacement and its statistical behaviour in terms of the scatter of the amplitudes between the time averages obtained from different trajectories. We especially demonstrate how anomalous dynamics may be identified for systems, which, on first sight, appear to be Brownian. Moreover, we discuss the ergodicity breaking parameters for the different anomalous stochastic processes and showcase the physical origins for the various behaviours. This Perspective is intended as a guidebook for both experimentalists and theorists working on systems, which exhibit anomalous diffusion. KW - intermittent chaotic systems KW - Fokker-Planck equations KW - time random-walks KW - fluorescence photobleaching recovery KW - fluctuation-dissipation theorem KW - fractional dynamics approach KW - photon-counting statistics KW - weak ergodicity breaking KW - flight search patterns KW - levy flights Y1 - 2014 U6 - https://doi.org/10.1039/c4cp03465a SN - 1463-9076 SN - 1463-9084 VL - 2014 IS - 16 SP - 24128 EP - 24164 ER - TY - JOUR A1 - Metzler, Ralf A1 - Jeon, Jae-Hyung A1 - Cherstvy, Andrey G. A1 - Barkai, Eli T1 - Anomalous diffusion models and their properties: non-stationarity, non-ergodicity, and ageing at the centenary of single particle tracking JF - Physical chemistry, chemical physics : a journal of European Chemical Societies N2 - Modern microscopic techniques following the stochastic motion of labelled tracer particles have uncovered significant deviations from the laws of Brownian motion in a variety of animate and inanimate systems. Such anomalous diffusion can have different physical origins, which can be identified from careful data analysis. In particular, single particle tracking provides the entire trajectory of the traced particle, which allows one to evaluate different observables to quantify the dynamics of the system under observation. We here provide an extensive overview over different popular anomalous diffusion models and their properties. We pay special attention to their ergodic properties, highlighting the fact that in several of these models the long time averaged mean squared displacement shows a distinct disparity to the regular, ensemble averaged mean squared displacement. In these cases, data obtained from time averages cannot be interpreted by the standard theoretical results for the ensemble averages. Here we therefore provide a comparison of the main properties of the time averaged mean squared displacement and its statistical behaviour in terms of the scatter of the amplitudes between the time averages obtained from different trajectories. We especially demonstrate how anomalous dynamics may be identified for systems, which, on first sight, appear to be Brownian. Moreover, we discuss the ergodicity breaking parameters for the different anomalous stochastic processes and showcase the physical origins for the various behaviours. This Perspective is intended as a guidebook for both experimentalists and theorists working on systems, which exhibit anomalous diffusion. Y1 - 2014 U6 - https://doi.org/10.1039/c4cp03465a SN - 1463-9076 SN - 1463-9084 VL - 16 IS - 44 SP - 24128 EP - 24164 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Talukder, Srijeeta A1 - Sen, Shrabani A1 - Chakraborti, Prantik A1 - Metzler, Ralf A1 - Banik, Suman K. A1 - Chaudhury, Pinaki T1 - Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA JF - The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr N2 - We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters is estimated for this purpose for three different DNA sequences. The analysis leads us to a better understanding of the sequence dependent nature of the breathing dynamics of hetero-polymeric DNA. Out of the 14 model parameters for DNA stability in the statistical Poland-Scheraga approach, the hydrogen bond interaction epsilon(hb)(AT) for an AT base pair and the ring factor. turn out to be the most sensitive parameters. In addition, the stacking interaction epsilon(st)(TA-TA) for an TA-TA nearest neighbor pair of base-pairs is found to be the most sensitive one among all stacking interactions. Moreover, we also establish that the nature of stacking interaction has a deciding effect on the DNA breathing dynamics, not the number of times a particular stacking interaction appears in a sequence. We show that the sensitivity analysis can be used as an effective measure to guide a stochastic optimization technique to find the kinetic rate constants related to the dynamics as opposed to the case where the rate constants are measured using the conventional unbiased way of optimization. (c) 2014 AIP Publishing LLC. Y1 - 2014 U6 - https://doi.org/10.1063/1.4869112 SN - 0021-9606 SN - 1089-7690 VL - 140 IS - 12 PB - American Institute of Physics CY - Melville ER - TY - JOUR A1 - Godec, Aljaz A1 - Bauer, Maximilian A1 - Metzler, Ralf T1 - Collective dynamics effect transient subdiffusion of inert tracers in flexible gel networks JF - New journal of physics : the open-access journal for physics N2 - Based on extensive Brownian dynamics simulations we study the thermal motion of a tracer bead in a cross-linked, flexible gel in the limit when the tracer particle size is comparable to or even larger than the equilibrium mesh size of the gel. The analysis of long individual trajectories of the tracer demonstrates the existence of pronounced transient anomalous diffusion. From the time averaged mean squared displacement and the time averaged van Hove correlation functions we elucidate the many-body origin of the non-Brownian tracer bead dynamics. Our results shed new light onto the ongoing debate over the physical origin of steric tracer interactions with structured environments. KW - anomalous diffusion KW - gel network KW - van Hove correlation Y1 - 2014 U6 - https://doi.org/10.1088/1367-2630/16/9/092002 SN - 1367-2630 VL - 16 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Sandev, Trifce A1 - Metzler, Ralf A1 - Tomovski, Zivorad T1 - Correlation functions for the fractional generalized Langevin equation in the presence of internal and external noise JF - Journal of mathematical physics N2 - We study generalized fractional Langevin equations in the presence of a harmonic potential. General expressions for the mean velocity and particle displacement, the mean squared displacement, position and velocity correlation functions, as well as normalized displacement correlation function are derived. We report exact results for the cases of internal and external friction, that is, when the driving noise is either internal and thus the fluctuation-dissipation relation is fulfilled or when the noise is external. The asymptotic behavior of the generalized stochastic oscillator is investigated, and the case of high viscous damping (overdamped limit) is considered. Additional behaviors of the normalized displacement correlation functions different from those for the regular damped harmonic oscillator are observed. In addition, the cases of a constant external force and the force free case are obtained. The validity of the generalized Einstein relation for this process is discussed. The considered fractional generalized Langevin equation may be used to model anomalous diffusive processes including single file-type diffusion. Y1 - 2014 U6 - https://doi.org/10.1063/1.4863478 SN - 0022-2488 SN - 1089-7658 VL - 55 IS - 2 PB - American Institute of Physics CY - Melville ER - TY - JOUR A1 - de Carvalho, Sidney J. A1 - Metzler, Ralf A1 - Cherstvy, Andrey G. T1 - Critical adsorption of polyelectrolytes onto charged Janus nanospheres JF - Physical chemistry, chemical physics : a journal of European Chemical Societies N2 - Based on extensive Monte Carlo simulations and analytical considerations we study the electrostatically driven adsorption of flexible polyelectrolyte chains onto charged Janus nanospheres. These net-neutral colloids are composed of two equally but oppositely charged hemispheres. The critical binding conditions for polyelectrolyte chains are analysed as function of the radius of the Janus particle and its surface charge density, as well as the salt concentration in the ambient solution. Specifically for the adsorption of finite-length polyelectrolyte chains onto Janus nanoparticles, we demonstrate that the critical adsorption conditions drastically differ when the size of the Janus particle or the screening length of the electrolyte are varied. We compare the scaling laws obtained for the adsorption-desorption threshold to the known results for uniformly charged spherical particles, observing significant disparities. We also contrast the changes to the polyelectrolyte chain conformations close to the surface of the Janus nanoparticles as compared to those for simple spherical particles. Finally, we discuss experimentally relevant physicochemical systems for which our simulations results may become important. In particular, we observe similar trends with polyelectrolyte complexation with oppositely but heterogeneously charged proteins. Y1 - 2014 U6 - https://doi.org/10.1039/c4cp02207f SN - 1463-9076 SN - 1463-9084 VL - 16 IS - 29 SP - 15539 EP - 15550 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Ghosh, Surya K. A1 - Cherstvy, Andrey G. A1 - Metzler, Ralf T1 - Deformation propagation in responsive polymer network films JF - The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr N2 - We study the elastic deformations in a cross-linked polymer network film triggered by the binding of submicron particles with a sticky surface, mimicking the interactions of viral pathogens with thin films of stimulus-responsive polymeric materials such as hydrogels. From extensive Langevin Dynamics simulations we quantify how far the network deformations propagate depending on the elasticity parameters of the network and the adhesion strength of the particles. We examine the dynamics of the collective area shrinkage of the network and obtain some simple relations for the associated characteristic decay lengths. A detailed analysis elucidates how the elastic energy of the network is distributed between stretching and compression modes in response to the particle binding. We also examine the force-distance curves of the repulsion or attraction interactions for a pair of sticky particles in the polymer network film as a function of the particle-particle separation. The results of this computational study provide new insight into collective phenomena in soft polymer network films and may, in particular, be applied to applications for visual detection of pathogens such as viruses via a macroscopic response of thin films of cross-linked hydrogels. (C) 2014 AIP Publishing LLC. Y1 - 2014 U6 - https://doi.org/10.1063/1.4893056 SN - 0021-9606 SN - 1089-7690 VL - 141 IS - 7 PB - American Institute of Physics CY - Melville ER - TY - JOUR A1 - Bauer, Maximilian A1 - Godec, Aljaz A1 - Metzler, Ralf T1 - Diffusion of finite-size particles in two-dimensional channels with random wall configurations JF - Physical chemistry, chemical physics : a journal of European Chemical Societies N2 - Diffusion of chemicals or tracer molecules through complex systems containing irregularly shaped channels is important in many applications. Most theoretical studies based on the famed Fick-Jacobs equation focus on the idealised case of infinitely small particles and reflecting boundaries. In this study we use numerical simulations to consider the transport of finite-size particles through asymmetrical two-dimensional channels. Additionally, we examine transient binding of the molecules to the channel walls by applying sticky boundary conditions. We consider an ensemble of particles diffusing in independent channels, which are characterised by common structural parameters. We compare our results for the long-time effective diffusion coefficient with a recent theoretical formula obtained by Dagdug and Pineda Y1 - 2014 U6 - https://doi.org/10.1039/c3cp55160a SN - 1463-9076 SN - 1463-9084 VL - 16 IS - 13 SP - 6118 EP - 6128 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Bauer, Maximilian A1 - Godec, Aljaž A1 - Metzler, Ralf T1 - Diffusion of finite-size particles in two-dimensional channels with random wall configurations JF - Physical chemistry, chemical physics : PCCP ; a journal of European chemical societies N2 - Diffusion of chemicals or tracer molecules through complex systems containing irregularly shaped channels is important in many applications. Most theoretical studies based on the famed Fick–Jacobs equation focus on the idealised case of infinitely small particles and reflecting boundaries. In this study we use numerical simulations to consider the transport of finite-size particles through asymmetrical two-dimensional channels. Additionally, we examine transient binding of the molecules to the channel walls by applying sticky boundary conditions. We consider an ensemble of particles diffusing in independent channels, which are characterised by common structural parameters. We compare our results for the long-time effective diffusion coefficient with a recent theoretical formula obtained by Dagdug and Pineda [J. Chem. Phys., 2012, 137, 024107]. KW - anomalous diffusion KW - fractional dynamics KW - transport KW - nonergodicity KW - coefficient Y1 - 2014 U6 - https://doi.org/10.1039/C3CP55160A SN - 1463-9084 SN - 1463-9076 VL - 16 IS - 13 SP - 6118 EP - 6128 PB - RSC Publications CY - Cambridge ER - TY - JOUR A1 - Krüsemann, Henning A1 - Godec, Aljaz A1 - Metzler, Ralf T1 - First-passage statistics for aging diffusion in systems with annealed and quenched disorder JF - Physical review : E, Statistical, nonlinear and soft matter physics N2 - Aging, the dependence of the dynamics of a physical process on the time t(a) since its original preparation, is observed in systems ranging from the motion of charge carriers in amorphous semiconductors over the blinking dynamics of quantum dots to the tracer dispersion in living biological cells. Here we study the effects of aging on one of the most fundamental properties of a stochastic process, the first-passage dynamics. We find that for an aging continuous time random walk process, the scaling exponent of the density of first-passage times changes twice as the aging progresses and reveals an intermediate scaling regime. The first-passage dynamics depends on t(a) differently for intermediate and strong aging. Similar crossovers are obtained for the first-passage dynamics for a confined and driven particle. Comparison to the motion of an aged particle in the quenched trap model with a bias shows excellent agreement with our analytical findings. Our results demonstrate how first-passage measurements can be used to unravel the age t(a) of a physical system. Y1 - 2014 U6 - https://doi.org/10.1103/PhysRevE.89.040101 SN - 1539-3755 SN - 1550-2376 VL - 89 IS - 4 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Goychuk, Igor A1 - Kharchenko, Vasyl O. A1 - Metzler, Ralf T1 - How Molecular Motors Work in the Crowded Environment of Living Cells: Coexistence and Efficiency of Normal and Anomalous Transport JF - PLoS one N2 - Recent experiments reveal both passive subdiffusion of various nanoparticles and anomalous active transport of such particles by molecular motors in the molecularly crowded environment of living biological cells. Passive and active microrheology reveals that the origin of this anomalous dynamics is due to the viscoelasticity of the intracellular fluid. How do molecular motors perform in such a highly viscous, dissipative environment? Can we explain the observed co-existence of the anomalous transport of relatively large particles of 100 to 500 nm in size by kinesin motors with the normal transport of smaller particles by the same molecular motors? What is the efficiency of molecular motors in the anomalous transport regime? Here we answer these seemingly conflicting questions and consistently explain experimental findings in a generalization of the well-known continuous diffusion model for molecular motors with two conformational states in which viscoelastic effects are included. Y1 - 2014 U6 - https://doi.org/10.1371/journal.pone.0091700 SN - 1932-6203 VL - 9 IS - 3 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Shin, Jaeoh A1 - Cherstvy, Andrey G. A1 - Metzler, Ralf ED - Metzler, Ralf T1 - Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size JF - Soft Matter N2 - The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible polymer chains in the presence of different degrees of crowding. From the analysis of the looping–unlooping rates and the looping probabilities of the chain ends we show that the presence of small crowders typically slows down the chain dynamics but larger crowders may in fact facilitate the looping. We rationalise these non-trivial and often counterintuitive effects of the crowder size on the looping kinetics in terms of an effective solution viscosity and standard excluded volume. It is shown that for small crowders the effect of an increased viscosity dominates, while for big crowders we argue that confinement effects (caging) prevail. The tradeoff between both trends can thus result in the impediment or facilitation of polymer looping, depending on the crowder size. We also examine how the crowding volume fraction, chain length, and the attraction strength of the contact groups of the polymer chain affect the looping kinetics and hairpin formation dynamics. Our results are relevant for DNA looping in the absence and presence of protein mediation, DNA hairpin formation, RNA folding, and the folding of polypeptide chains under biologically relevant high-crowding conditions. KW - gene-regulation kinetics KW - physiological consequences KW - spatial-organization KW - anomalous diffusion KW - folding kinetics KW - living cells KW - dna coiling KW - in-vitro KW - dynamics KW - mixtures Y1 - 2014 SN - 1744-683X SP - 472 EP - 488 PB - The Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Palyulin, Vladimir V. A1 - Chechkin, Aleksei V. A1 - Metzler, Ralf T1 - Levy flights do not always optimize random blind search for sparse targets JF - Proceedings of the National Academy of Sciences of the United States of America N2 - It is generally believed that random search processes based on scale-free, Levy stable jump length distributions (Levy flights) optimize the search for sparse targets. Here we show that this popular search advantage is less universal than commonly assumed. We study the efficiency of a minimalist search model based on Levy flights in the absence and presence of an external drift (underwater current, atmospheric wind, a preference of the walker owing to prior experience, or a general bias in an abstract search space) based on two different optimization criteria with respect to minimal search time and search reliability (cumulative arrival probability). Although Levy flights turn out to be efficient search processes when the target is far from the starting point, or when relative to the starting point the target is upstream, we show that for close targets and for downstream target positioning regular Brownian motion turns out to be the advantageous search strategy. Contrary to claims that Levy flights with a critical exponent alpha = 1 are optimal for the search of sparse targets in different settings, based on our optimization parameters the optimal a may range in the entire interval (1, 2) and especially include Brownian motion as the overall most efficient search strategy. KW - search optimization KW - stochastic processes KW - Levy foraging hypothesis Y1 - 2014 U6 - https://doi.org/10.1073/pnas.1320424111 SN - 0027-8424 VL - 111 IS - 8 SP - 2931 EP - 2936 PB - National Acad. of Sciences CY - Washington ER - TY - JOUR A1 - Godec, Aljaz A1 - Chechkin, Aleksei V. A1 - Barkai, Eli A1 - Kantz, Holger A1 - Metzler, Ralf T1 - Localisation and universal fluctuations in ultraslow diffusion processes JF - Journal of physics : A, Mathematical and theoretical N2 - We study ultraslow diffusion processes with logarithmic mean squared displacement (MSD) < x(2)(t)> similar or equal to log(gamma)t. Comparison of annealed (renewal) continuous time random walks (CTRWs) with logarithmic waiting time distribution psi(tau) similar or equal to 1/(tau log(1+gamma)tau) and Sinai diffusion in quenched random landscapes reveals striking similarities, despite the great differences in their physical nature. In particular, they exhibit a weakly non-ergodic disparity of the time-averaged and ensemble-averaged MSDs. Remarkably, for the CTRW we observe that the fluctuations of time averages become universal, with an exponential suppression of mobile trajectories. We discuss the fundamental connection between the Golosov localization effect and non-ergodicity in the sense of the disparity between ensemble-averaged MSD and time-averaged MSD. KW - Sinai diffusion KW - anomalous diffusion KW - quenched energy landscape Y1 - 2014 U6 - https://doi.org/10.1088/1751-8113/47/49/492002 SN - 1751-8113 SN - 1751-8121 VL - 47 IS - 49 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Shin, Jaeoh A1 - Cherstvy, Andrey G. A1 - Metzler, Ralf T1 - Mixing and segregation of ring polymers: spatial confinement and molecular crowding effects JF - New journal of physics : the open-access journal for physics N2 - During the life cycle of bacterial cells the non-mixing of the two ring-shaped daughter genomes is an important prerequisite for the cell division process. Mimicking the environments inside highly crowded biological cells, we study the dynamics and statistical behavior of two flexible ring polymers in the presence of cylindrical confinement and crowding molecules. From extensive computer simulations we determine the degree of ring-ring overlap and the number of inter-monomer contacts for varying volume fractions phi of crowders. We also examine the entropic demixing of polymer rings in the presence of mobile crowders and determine the characteristic times of the internal polymer dynamics. Effects of the ring length on ring-ring overlap are also analyzed. In particular, on systematic variation of the fraction of crowding molecules, a (1 - phi)-scaling is found for the ring-ring overlap length along the cylinder axis, and a non-monotonic dependence of the 3D ring-ring contact number with a maximum at phi approximate to 0.2 is obtained. Our results demonstrate that polymer rings are demixed and separated by particular entropy-favourable partitioning of crowders along the axis of the cylindrical simulation box. These findings help to rationalize the implications of macromolecular crowding for circular DNA molecules in confined spaces inside bacteria as well as in localized cellular compartments inside eukaryotic cells. KW - polymers KW - confinement KW - crowding Y1 - 2014 U6 - https://doi.org/10.1088/1367-2630/16/5/053047 SN - 1367-2630 VL - 16 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Goychuk, Igor A1 - Kharchenko, Vasyl O. A1 - Metzler, Ralf T1 - Molecular motors pulling cargos in the viscoelastic cytosol: how power strokes beat subdiffusion JF - Physical chemistry, chemical physics : a journal of European Chemical Societies N2 - The discovery of anomalous diffusion of larger biopolymers and submicron tracers such as endogenous granules, organelles, or virus capsids in living cells, attributed to the viscoelastic nature of the cytoplasm, provokes the question whether this complex environment equally impacts the active intracellular transport of submicron cargos by molecular motors such as kinesins: does the passive anomalous diffusion of free cargo always imply its anomalously slow active transport by motors, the mean transport distance along microtubule growing sublinearly rather than linearly in time? Here we analyze this question within the widely used two-state Brownian ratchet model of kinesin motors based on the continuous-state diffusion along microtubules driven by a flashing binding potential, where the cargo particle is elastically attached to the motor. Depending on the cargo size, the loading force, the amplitude of the binding potential, the turnover frequency of the molecular motor enzyme, and the linker stiffness we demonstrate that the motor transport may turn out either normal or anomalous, as indeed measured experimentally. We show how a highly efficient normal active transport mediated by motors may emerge despite the passive anomalous diffusion of the cargo, and study the intricate effects of the elastic linker. Under different, well specified conditions the microtubule-based motor transport becomes anomalously slow and thus significantly less efficient. Y1 - 2014 U6 - https://doi.org/10.1039/c4cp01234h SN - 1463-9076 SN - 1463-9084 VL - 16 IS - 31 SP - 16524 EP - 16535 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Goychuk, Igor A. A1 - Kharchenko, Vasyl O. A1 - Metzler, Ralf T1 - Molecular motors pulling cargos in the viscoelastic cytosol: how power strokes beat subdiffusion JF - Physical Chemistry Chemical Physics N2 - The discovery of anomalous diffusion of larger biopolymers and submicron tracers such as endogenous granules, organelles, or virus capsids in living cells, attributed to the viscoelastic nature of the cytoplasm, provokes the question whether this complex environment equally impacts the active intracellular transport of submicron cargos by molecular motors such as kinesins: does the passive anomalous diffusion of free cargo always imply its anomalously slow active transport by motors, the mean transport distance along microtubule growing sublinearly rather than linearly in time? Here we analyze this question within the widely used two-state Brownian ratchet model of kinesin motors based on the continuous-state diffusion along microtubules driven by a flashing binding potential, where the cargo particle is elastically attached to the motor. Depending on the cargo size, the loading force, the amplitude of the binding potential, the turnover frequency of the molecular motor enzyme, and the linker stiffness we demonstrate that the motor transport may turn out either normal or anomalous, as indeed measured experimentally. We show how a highly efficient normal active transport mediated by motors may emerge despite the passive anomalous diffusion of the cargo, and study the intricate effects of the elastic linker. Under different, well specified conditions the microtubule-based motor transport becomes anomalously slow and thus significantly less efficient. KW - royal soc chemistry KW - thomas graham house KW - science park KW - milton rd KW - cambridge cb4 0wf KW - cambs KW - england Y1 - 2014 SN - 1463-9076 IS - 16 SP - 16524 EP - 16535 PB - the Royal Society of Chemistry CY - Cambridge ER -