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Ralf Metzler

Publications and source records attributed to Ralf Metzler.

215 records · Page 12Linked to original sources

Tight and loose shapes in flat entangled dense polymers

We investigate the effects of topological constraints (entanglements) on two dimensional polymer loops in the dense phase, and at the collapse transition (Theta point). Previous studies have shown that in the dilute phase the entangled region becomes tight, and is thus localised on a small portion of the polymer. We find that the entropic force favouring tightness is considerably weaker in dense polymers. While the simple figure-eight structure, created by a single crossing in the polymer loop, localises weakly, the trefoil knot and all other prime knots are loosely spread out over the entire chain. In both the dense and Theta conditions, the uncontracted knot configuration is the most likely shape within a scaling analysis. By contrast, a strongly localised figure-eight is the most likely shape for dilute prime knots. Our findings are compared to recent simulations.

cond-mat.soft↗

First passage and arrival time densities for Lévy flights and the failure of the method of images

We discuss the first passage time problem in the semi-infinite interval, for homogeneous stochastic Markov processes with L{é}vy stable jump length distributions $λ(x)\sim\ell^α/|x|^{1+α}$ ($|x|\gg\ell$), namely, L{é}vy flights (LFs). In particular, we demonstrate that the method of images leads to a result, which violates a theorem due to Sparre Andersen, according to which an arbitrary continuous and symmetric jump length distribution produces a first passage time density (FPTD) governed by the universal long-time decay $\sim t^{-3/2}$. Conversely, we show that for LFs the direct definition known from Gaussian processes in fact defines the probability density of first arrival, which for LFs differs from the FPTD. Our findings are corroborated by numerical results.

cond-mat.stat-mech↗

Bubble dynamics in DNA

The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example for conformational changes of biological macromolecules. We study the dynamics of bubble formation in terms of a Fokker-Planck equation for the probability density to find a bubble of size n base pairs at time t, on the basis of the free energy in the Poland-Scheraga model. Characteristic bubble closing and opening times can be determined from the corresponding first passage time problem, and are sensitive to the specific parameters entering the model. A multistate unzipping model with constant rates recently applied to DNA breathing dynamics [G. Altan-Bonnet et al, Phys. Rev. Lett. 90, 138101 (2003)] emerges as a limiting case.

cond-mat.soft↗

When translocation dynamics becomes anomalous

Recent single molecule experiments probing the passage process of a short single-stranded DNA (ssDNA) through a membrane channel (translocation) allow to measure the passage time distribution. Building on a recent modelling approach (D. K. Lubensky and D. R. Nelson, Biophys. J. 77, 1824 (1999)), which has been demonstrated to be valid for chains of up to $\simeq 300$ nucleotides and therefore well applies to the system we have in mind, we discuss the consequences if the associated dynamics is not of Markov origin, but if strong memory effects prevail during the translocation. Motivation is drawn from recent results indicating that the distribution of translocation times is broader than predicted by simple Markovian models based on Brownian motion.

cond-mat.stat-mech↗

Lévy flights in a steep potential well

Lévy flights in steeper than harmonic potentials have been shown to exhibit finite variance and a critical time at which a bifurcation from an initial mono-modal to a terminal bimodal distribution occurs (Chechkin et al., Phys. Rev. E {\bf 67}, 010102(R) (2003)). In this paper, we present a detailed study of Lévy flights in potentials of the type U(x)∝|x|^c with c>2. Apart from the bifurcation into bimodality, we find the interesting result that for c>4 a trimodal transient exists due to the temporal overlap between the decay of the central peak around the initial $δ$-condition and the building up of the two emerging side-peaks, which are characteristic for the stationary state. Thus, for certain system parameters there exists a transient tri-modal distribution of the Lévy flight. These properties of LFs in external potentials of the power-law type can be represented by certain phase diagrams. We also present details about the proof of multi-modality and the numerical procedures to establish the probability distribution of the process.

cond-mat.stat-mech↗

Comment on "Why is the DNA denaturation transition first order?"

In this comment we argue that while the conclusions in the original paper (Y. Kafri, D. Mukamel and L. Peliti, Phys. Rev. Lett. 85, 4988 (2000)) are correct for asymptotically long DNA chains, they do not apply to the chains used in typical experiments. In the added last paragraph, we point out that for real DNA the average distance between denatured loops is not of the order of the persistence length of a single-stranded chain but much larger. This corroborates our reasoning that the double helix between loops is quite rigid, and thereby our conclusion.

cond-mat.stat-mech↗

Entropy loss in long-distance DNA looping

The entropy loss due to the formation of one or multiple loops in circular and linear DNA chains is calculated from a scaling approach in the limit of long chain segments. The analytical results allow to obtain a fast estimate for the entropy loss for a given configuration. Numerical values obtained for some examples suggest that the entropy loss encountered in loop closure in typical genetic switches may become a relevant factor which has to be overcome by the released bond energy between the looping contact sites.

cond-mat.stat-mech↗

Towards deterministic equations for Levy walks: the fractional material derivative

Levy walks are random processes with an underlying spatiotemporal coupling. This coupling penalizes long jumps, and therefore Levy walks give a proper stochastic description for a particle's motion with broad jump length distribution. We derive a generalized dynamical formulation for Levy walks in which the fractional equivalent of the material derivative occurs. Our approach will be useful for the dynamical formulation of Levy walks in an external force field or in phase space for which the description in terms of the continuous time random walk or its corresponding generalized master equation are less well suited.

cond-mat.stat-mech↗

Force-Extension Relations for Polymers with Sliding Links

Topological entanglements in polymers are mimicked by sliding rings (slip-links) which enforce pair contacts between monomers. We study the force-extension curve for linear polymers in which slip-links create additional loops of variable size. For a single loop in a phantom chain, we obtain exact expressions for the average end-to-end separation: The linear response to a small force is related to the properties of the unstressed chain, while for a large force the polymer backbone can be treated as a sequence of Pincus--de Gennes blobs, the constraint effecting only a single blob. Generalizing this picture, scaling arguments are used to include self-avoiding effects.

cond-mat.stat-mech↗

Towards the molecular workshop: entropy-driven designer molecules, entropy activation, and nanomechanical devices

We introduce some basic concepts for designer molecules with functional units which are driven by entropic rather than energetic forces. This idea profits from the mechanically interlocked nature of topological molecules such as catenanes and rotaxanes, which allows for mobile elements whose accessible configuration space gives rise to entropic intramolecular forces. Such entropy-driven designer molecules open the possibility for externally controllable functional molecules and nanomechanical devices.

cond-mat.stat-mech↗

Physical Pictures of Transport in Heterogeneous Media: Advection-Dispersion, Random Walk and Fractional Derivative Formulations

The basic conceptual picture and theoretical basis for development of transport equations in porous media are examined. The general form of the governing equations is derived for conservative chemical transport in heterogeneous geological formations, for single realizations and for ensemble averages of the domain. The application of these transport equations is focused on accounting for the appearance of non-Fickian (anomalous) transport behavior. The general ensemble-averaged transport equation is shown to be equivalent to a continuous time random walk (CTRW) and reduces to the conventional forms of the advection-dispersion equation (ADE) under highly restrictive conditions. Fractional derivative formulations of the transport equations, both temporal and spatial, emerge as special cases of the CTRW. In particular, the use in this context of L{é}vy flights is critically examined. In order to determine chemical transport in field-scale situations, the CTRW approach is generalized to non-stationary systems. We outline a practical numerical scheme, similar to those used with extended geological models, to account for the often important effects of unresolved heterogeneities.

cond-mat.stat-mech↗

Tightness of slip-linked polymer chains

We study the interplay between entropy and topological constraints for a polymer chain in which sliding rings (slip-links) enforce pair contacts between monomers. These slip-links divide a closed ring polymer into a number of sub-loops which can exchange length between each other. In the ideal chain limit, we find the joint probability density function for the sizes of segments within such a slip-linked polymer chain (paraknot). A particular segment is tight (small in size) or loose (of the order of the overall size of the paraknot) depending on both the number of slip-links it incorporates and its competition with other segments. When self-avoiding interactions are included, scaling arguments can be used to predict the statistics of segment sizes for certain paraknot configurations.

cond-mat.stat-mech↗

Diffusion on random site percolation clusters. Theory and NMR microscopy experiments with model objects

Quasi two-dimensional random site percolation model objects were fabricate based on computer generated templates. Samples consisting of two compartments, a reservoir of H$_2$O gel attached to a percolation model object which was initially filled with D$_2$O, were examined with NMR (nuclear magnetic resonance) microscopy for rendering proton spin density maps. The propagating proton/deuteron inter-diffusion profiles were recorded and evaluated with respect to anomalous diffusion parameters. The deviation of the concentration profiles from those expected for unobstructed diffusion directly reflects the anomaly of the propagator for diffusion on a percolation cluster. The fractal dimension of the random walk, $d_w$, evaluated from the diffusion measurements on the one hand and the fractal dimension, $d_f$, deduced from the spin density map of the percolation object on the other permits one to experimentally compare dynamical and static exponents. Approximate calculations of the propagator are given on the basis of the fractional diffusion equation. Furthermore, the ordinary diffusion equation was solved numerically for the corresponding initial and boundary conditions for comparison. The anomalous diffusion constant was evaluated and is compared to the Brownian case. Some ad hoc correction of the propagator is shown to pay tribute to the finiteness of the system. In this way, anomalous solutions of the fractional diffusion equation could experimentally be verified for the first time.

cond-mat↗

Equilibrium shapes of flat knots

We study the equilibrium shapes of prime and composite knots confined to two dimensions. Using rigorous scaling arguments we show that, due to self-avoiding effects, the topological details of prime knots are localised on a small portion of the larger ring polymer. Within this region, the original knot configuration can assume a hierarchy of contracted shapes, the dominating one given by just one small loop. This hierarchy is investigated in detail for the flat trefoil knot, and corroborated by Monte Carlo simulations.

cond-mat.stat-mech↗

The future is noisy: on the role of spatial fluctuations in genetic switching

A genetic switch may be realised by a certain operator sector on the DNA strand from which either genetic code, to the left or to the right of this operator sector, can be transcribed and the corresponding information processed. This switch is controlled by messenger molecules, i.e., they determine to which side the switch is flipped. Recently, it has been realised that noise plays an elementary role in genetic switching, and the effect of number fluctuations of the messenger molecules have been explored. Here we argue that the assumption of well-stirredness taken in the previous models may not be sufficient to characterise the influence of noise: {\em spatial} fluctuations play a non-negligible part in cellular genetic switching processes.

cond-mat.stat-mech↗

Fractional Klein-Kramers equation for superdiffusive transport: normal versus anomalous time evolution in a differential L{é}vy walk model

We introduce a fractional Klein-Kramers equation which describes sub-ballistic superdiffusion in phase space in the presence of a space-dependent external force field. This equation defines the differential L{é}vy walk model whose solution is shown to be non-negative. In the velocity coordinate, the probability density relaxes in Mittag-Leffler fashion towards the Maxwell distribution whereas in the space coordinate, no stationary solution exists and the temporal evolution of moments exhibits a competition between Brownian and anomalous contributions.

cond-mat.stat-mech↗

Levy Flights in External Force Fields: Langevin and Fractional Fokker-Planck Equations, and their Solutions

We consider Levy flights subject to external force fields. This anomalous transport process is described by two approaches, a Langevin equation with Levy noise and the corresponding generalized Fokker-Planck equation containing a fractional derivative in space. The cases of free flights, constant force and linear Hookean force are analyzed in detail, and we corroborate our findings with results from numerical simulations. We discuss the non-Gibbsian character of the stationary solution for the case of the Hookean force, i.e. the deviation from Boltzmann equilibrium for long times. The possible connection to Tsallis's q-statistics is studied.

cond-mat.stat-mech↗