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Ralf Metzler

Publications and source records attributed to Ralf Metzler.

At least 145 records · Page 8Linked to original sources

Aging dynamics in interacting many-body systems

Low-dimensional, complex systems are often characterized by logarithmically slow dynamics. We study the generic motion of a labeled particle in an ensemble of identical diffusing particles with hardcore interactions in a strongly disordered, one-dimensional environment. Each particle in this single file is trapped for a random waiting time $τ$ with power law distribution $ψ(τ)\simeqτ^{-1- α}$, such that the $τ$ values are independent, local quantities for all particles. From scaling arguments and simulations, we find that for the scale-free waiting time case $0<α<1$, the tracer particle dynamics is ultra-slow with a logarithmic mean square displacement (MSD) $\langle x^2(t)\rangle\simeq(\log t)^{1/2}$. This extreme slowing down compared to regular single file motion $\langle x^2(t)\rangle\simeq t^{1/2}$ is due to the high likelihood that the labeled particle keeps encountering strongly immobilized neighbors. For the case $1<α<2$ we observe the MSD scaling $\langle x^2(t)\rangle\simeq t^γ$, where $γ<1/2$, while for $α>2$ we recover Harris law $\simeq t^{1/2}$.

physics.chem-ph↗

Particle invasion, survival, and non-ergodicity in 2D diffusion processes with space-dependent diffusivity

We study the thermal Markovian diffusion of tracer particles in a 2D medium with spatially-varying diffusivity $D(r)$, mimicking recently measured, heterogeneous maps of the apparent diffusion coefficient in biological cells. For this heterogeneous diffusion process (HDP) we analyse the mean squared displacement (MSD) of the tracer particles, the time averaged MSD, the spatial probability density function, and the first passage time dynamics from the cell boundary to the nucleus. Moreover we examine the non-ergodic properties of this process which are important for the correct physical interpretation of time averages of observables obtained from single particle tracking experiments. From extensive computer simulations of the 2D stochastic Langevin equation we present an in-depth study of this HDP. In particular, we find that the MSDs along the radial and azimuthal directions in a circular domain obey anomalous and Brownian scaling, respectively. We demonstrate that the time averaged MSD stays linear as a function of the lag time and the system thus reveals a weak ergodicity breaking. Our results will enable one to rationalise the diffusive motion of larger tracer particles such as viruses or submicron beads in biological cells.

cond-mat.stat-mech↗

Speeding up the first-passage for subdiffusion by introducing a finite potential barrier

We show that for a subdiffusive continuous time random walk with scale-free waiting time distribution the first-passage dynamics on a finite interval can be optimised by introduction of a piecewise linear potential barrier. Analytical results for the survival probability and first-passage density based on the fractional Fokker-Planck equation are shown to agree well with Monte Carlo simulations results. As an application we discus an improved deign for efficient translocation of gradient copolymers compared to homopolymer translocation in a quasi-equilibrium approximation.

cond-mat.stat-mech↗

Stochastic Optimization Based Study of Dimerization Kinetics

We investigate the potential of numerical algorithms to decipher the kinetic parameters involved in multi-step chemical reactions. To this end we study a dimerization kinetics of protein as a model system. We follow the dimerization kinetics using a stochastic simulation algorithm and combine it with three different optimization techniques (Genetic Algorithm, Simulated Annealing and Parallel Tempering) to obtain the rate constants involved in each reaction step. We find good convergence of the numerical scheme to the rate constants of the process. We also perform a sensitivity test on the reaction kinetic parameters to see the relative effects of the parameters for the associated profile of the monomer/dimer distribution.

physics.bio-ph↗

Sensing viruses by mechanical tension of DNA in responsive hydrogels

The rapid worldwide spread of severe viral infections, often involving novel modifications of viruses, poses major challenges to our health care systems. This means that tools that can efficiently and specifically diagnose viruses are much needed. To be relevant for a broad application in local health care centers, such tools should be relatively cheap and easy to use. Here we discuss the biophysical potential for the macroscopic detection of viruses based on the induction of a mechanical stress in a bundle of pre-stretched DNA molecules upon binding of viruses to the DNA. We show that the affinity of the DNA to the charged virus surface induces a local melting of the double-helix into two single-stranded DNA. This process effects a mechanical stress along the DNA chains leading to an overall contraction of the DNA. Our results suggest that when such DNA bundles are incorporated in a supporting matrix such as a responsive hydrogel, the presence of viruses may indeed lead to a significant, macroscopic mechanical deformation of the matrix. We discuss the biophysical basis for this effect and characterize the physical properties of the associated DNA melting transition. In particular, we reveal several scaling relations between the relevant physical parameters of the system. We promote this DNA-based assay for efficient and specific virus screening.

q-bio.BM↗

Aging renewal theory and application to random walks

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. We here 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]. 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.

cond-mat.stat-mech↗

Quantification of noise in the bifunctionality-induced post-translational modification

We present a generic analytical scheme for the quantification of fluctuations due to bifunctionality-induced signal transduction within the members of bacterial two-component system. The proposed model takes into account post-translational modifications in terms of elementary phosphotransfer kinetics. Sources of fluctuations due to autophosphorylation, kinase and phosphatase activity of the sensor kinase have been considered in the model via Langevin equations, which are then solved within the framework of linear noise approximation. The resultant analytical expression of phosphorylated response regulators are then used to quantify the noise profile of biologically motivated single and branched pathways. Enhancement and reduction of noise in terms of extra phosphate outflux and influx, respectively, have been analyzed for the branched system. Furthermore, role of fluctuations of the network output in the regulation of a promoter with random activation/deactivation dynamics has been analyzed.

q-bio.SC↗

Numerical approach to unbiased and driven generalized elastic model

From scaling arguments and numerical simulations, we investigate the properties of the generalized elastic model (GEM), that is used to describe various physical systems such as polymers, membranes, single-file systems, or rough interfaces. We compare analytical and numerical results for the subdiffusion exponent beta characterizing the growth of the mean squared displacement <(delta h)^2> of the field h described by the GEM dynamic equation. We study the scaling properties of the qth order moments <|delta h|^q> with time, finding that the interface fluctuations show no intermittent behavior. We also investigate the ergodic properties of the process h in terms of the ergodicity breaking parameter and the distribution of the time averaged mean squared displacement. Finally, we study numerically the driven GEM with a constant, localized perturbation and extract the characteristics of the average drift for a tagged probe.

cond-mat.stat-mech↗

Correlated continuous-time random walks: combining scale-invariance with long-range memory for spatial and temporal dynamics

Standard continuous time random walk (CTRW) models are renewal processes in the sense that at each jump a new, independent pair of jump length and waiting time are chosen. Globally, anomalous diffusion emerges through action of the generalized central limit theorem leading to scale-free forms of the jump length or waiting time distributions. Here we present a modified version of recently proposed correlated CTRW processes, where we incorporate a power-law correlated noise on the level of both jump length and waiting time dynamics. We obtain a very general stochastic model, that encompasses key features of several paradigmatic models of anomalous diffusion: discontinuous, scale-free displacements as in Levy flights, scale-free waiting times as in subdiffusive CTRWs, and the long-range temporal correlations of fractional Brownian motion (FBM). We derive the exact solutions for the single-time probability density functions and extract the scaling behaviours. Interestingly, we find that different combinations of the model parameters lead to indistinguishable shapes of the emerging probability density functions and identical scaling laws. Our model will be useful to describe recent experimental single particle tracking data, that feature a combination of CTRW and FBM properties.

cond-mat.stat-mech↗

Population splitting, trapping, and non-ergodicity in heterogeneous diffusion processes

We consider diffusion processes with a spatially varying diffusivity giving rise to anomalous diffusion. Such heterogeneous diffusion processes are analysed for the cases of exponential, power-law, and logarithmic dependencies of the diffusion coefficient on the particle position. Combining analytical approaches with stochastic simulations, we show that the functional form of the space-dependent diffusion coefficient and the initial conditions of the diffusing particles are vital for their statistical and ergodic properties. In all three cases a weak ergodicity breaking between the time and ensemble averaged mean squared displacements is observed. We also demonstrate a population splitting of the time averaged traces into fast and slow diffusers for the case of exponential variation of the diffusivity as well as a particle trapping in the case of the logarithmic diffusivity. Our analysis is complemented by the quantitative study of the space coverage, the diffusive spreading of the probability density, as well as the survival probability.

cond-mat.stat-mech↗

Transient ageing in fractional Brownian and Langevin equation motion

Stochastic processes driven by stationary fractional Gaussian noise, that is, fractional Brownian motion and fractional Langevin equation motion, are usually considered to be ergodic in the sense that, after an algebraic relaxation, time and ensemble averages of physical observables coincide. Recently it was demonstrated that fractional Brownian motion and fractional Langevin equation motion under external confinement are transiently non-ergodic---time and ensemble averages behave differently---from the moment when the particle starts to sense the confinement. Here we show that these processes also exhibit transient ageing, that is, physical observables such as the time averaged mean squared displacement depend on the time lag between the initiation of the system at time $t=0$ and the start of the measurement at the ageing time $t_a$. In particular, it turns out that for fractional Langevin equation motion the ageing dependence on $t_a$ is different between the cases of free and confined motion. We obtain explicit analytical expressions for the aged moments of the particle position as well as the time averaged mean squared displacement and present a numerical analysis of this transient ageing phenomenon.

cond-mat.stat-mech↗

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↗

Searching with and against the stream: Levy or Brown?

We study the efficiency of search processes based on Levy flights (LFs) with power-law distributed jump lengths in the presence of an external drift. While LFs turn out to be efficient search processes when relative to the starting point the target is upstream, in the downstream scenario regular Brownian motion turns out to be advantageous. This is caused by the occurrence of leapovers of LFs, due to which LFs typically overshoot a point in space. We establish criteria when the combination of the external stream and the initial distance between the starting point and the target favors LFs over regular Brownian search. Contrary to the common belief that LFs with a stable index alpha=1 are optimal, we find that the optimal alpha may range in the entire interval (1,2) and even include Brownian motion as the overall most efficient search strategy.

cond-mat.stat-mech↗

Distance matters: the impact of gene proximity in bacterial gene regulation

Following recent discoveries of colocalization of downstream-regulating genes in living cells, the impact of the spatial distance between such genes on the kinetics of gene product formation is increasingly recognized. We here show from analytical and numerical analysis that the distance between a transcription factor (TF) gene and its target gene drastically affects the speed and reliability of transcriptional regulation in bacterial cells. For an explicit model system we develop a general theory for the interactions between a TF and a transcription unit. The observed variations in regulation efficiency are linked to the magnitude of the variation of the TF concentration peaks as a function of the binding site distance from the signal source. Our results support the role of rapid binding site search for gene colocalization and emphasize the role of local concentration differences.

q-bio.SC↗

Transition dynamics in aging systems: microscopic origin of logarithmic time evolution

There exists compelling experimental evidence in numerous systems for logarithmically slow time evolution, yet its theoretical understanding remains elusive. We here introduce and study a generic transition process in complex systems, based on non-renewal, aging waiting times. Each state n of the system follows a local clock initiated at t=0. The random time τbetween clock ticks follows the waiting time density ψ(τ). Transitions between states occur only at local clock ticks and are hence triggered by the local forward waiting time, rather than by ψ(τ). For power-law forms ψ(τ) ~ τ^{-1-α} (0<α<1) we obtain a logarithmic time evolution of the state number ~ log(t/t_0), while for α>2 the process becomes normal in the sense that ~ t. In the intermediate range 1<α<2 we find the power-law growth ~ t^{α-1}. Our model provides a universal description for transition dynamics between aging and non-aging states.

cond-mat.stat-mech↗

Anomalous diffusion and ergodicity breaking in heterogeneous diffusion processes

We demonstrate the non-ergodicity of a simple Markovian stochastic processes with space-dependent diffusion coefficient $D(x)$. For power-law forms $D(x) \simeq|x|^α$, this process yield anomalous diffusion of the form $\ < x^2(t)\ > \simeq t^{2/(2-α)}$. Interestingly, in both the sub- and superdiffusive regimes we observe weak ergodicity breaking: the scaling of the time averaged mean squared displacement $\{δ^2}$ remains \emph{linear} and thus differs from the corresponding ensemble average $\ $. We analyze the non-ergodic behavior of this process in terms of the ergodicity breaking parameters and the distribution of amplitude scatter of $\{δ^2}$. This model represents an alternative approach to non-ergodic, anomalous diffusion that might be particularly relevant for diffusion in heterogeneous media.

cond-mat.stat-mech↗

In vivo facilitated diffusion model

Under dilute in vitro conditions transcription factors rapidly locate their target sequence on DNA by using the facilitated diffusion mechanism. However, whether this strategy of alternating between three-dimensional bulk diffusion and one-dimensional sliding along the DNA contour is still beneficial in the crowded interior of cells is highly disputed. Here we use a simple model for the bacterial genome inside the cell and present a semi-analytical model for the in vivo target search of transcription factors within the facilitated diffusion framework. Without having to resort to extensive simulations we determine the mean search time of a lac repressor in a living E. coli cell by including parameters deduced from experimental measurements. The results agree very well with experimental findings, and thus the facilitated diffusion picture emerges as a quantitative approach to gene regulation in living bacteria cells. Furthermore we see that the search time is not very sensitive to the parameters characterizing the DNA configuration and that the cell seems to operate very close to optimal conditions for target localization. Local searches as implied by the colocalization mechanism are only found to mildly accelerate the mean search time within our model.

q-bio.SC↗

The RARE model: a generalized approach to random relaxation processes in disordered systems

This paper introduces and analyses a general statistical model, termed the RARE model, of random relaxation processes in disordered systems. The model considers excitations, that are randomly scattered around a reaction center in a general embedding space. The model's input quantities are the spatial scattering statistics of the excitations around the reaction center, and the chemical reaction rates between the excitations and the reaction center as a function of their mutual distance. The framework of the RARE model is robust, and a detailed stochastic analysis of the random relaxation processes is established. Analytic results regarding the duration and the range of the random relaxation processes, as well as the model's thermodynamic limit, are obtained in closed form. In particular, the case of power-law inputs, which turn out to yield stretched exponential relaxation patterns and asymptotically Paretian relaxation ranges, is addressed in detail.

cond-mat.stat-mech↗