Non-Markovian closure kinetics of flexible polymers with hydrodynamic interactions.

This paper presents a theoretical analysis of the closure kinetics of a polymer with hydrodynamic interactions. This analysis, which takes into account the non-Markovian dynamics of the end-to-end vector and relies on the preaveraging of the mobility tensor (Zimm dynamics), is shown to reproduce very accurately the results of numerical simulations of the complete nonlinear dynamics. It is found that Markovian treatments based on a Wilemski-Fixman approximation significantly overestimate cyclization times (up to a factor 2), showing the importance of memory effects in the dynamics. In addition, this analysis provides scaling laws of the mean first cyclization time (MFCT) with the polymer size N and capture radius b, which are identical in both Markovian and non-Markovian approaches. In particular, it is found that the scaling of the MFCT for large N is given by T ∼ N(3/2)ln(N/b(2)), which differs from the case of the Rouse dynamics where T ∼ N(2). The extension to the case of the reaction kinetics of a monomer of a Zimm polymer with an external target in a confined volume is also presented.

Cyclization kinetics of Gaussian semiflexible polymer chains.

We consider the dynamics and the cyclization kinetics of Gaussian semiflexible chains, in which the interaction potential tends to align successive bonds. We provide asymptotic expressions for the cyclization time, for the eigenvalues and eigenfunctions, and for the mean square displacement at all time and length scales, with explicit dependence on the capture radius, on the positions of the reactive monomers in the chain, and on the finite number of beads. For the cyclization kinetics, we take into account non-Markovian effects by calculating the distribution of reactive conformations of the polymer, which are not taken into account in the classical Wilemski-Fixman theory. Comparison with numerical simulations confirms the accuracy of this non-Markovian theory.

Continuous-time random-walk approach to supercooled liquids. I. Different definitions of particle jumps and their consequences.

Single-particle trajectories in supercooled liquids display long periods of localization interrupted by "fast moves." This observation suggests a modeling by a continuous-time random walk (CTRW). We perform molecular dynamics simulations of equilibrated short-chain polymer melts near the critical temperature of mode-coupling theory Tc and extract "moves" from the monomer trajectories. We show that not all moves comply with the conditions of a CTRW. Strong forward-backward correlations are found in the supercooled state. A refinement procedure is suggested to exclude these moves from the analysis. We discuss the repercussions of the refinement on the jump-length and waiting-time distributions as well as on characteristic time scales, such as the average waiting time ("exchange time") and the average time for the first move ("persistence time"). The refinement modifies the temperature (T) dependence of these time scales. For instance, the average waiting time changes from an Arrhenius-type to a Vogel-Fulcher-type T dependence. We discuss this observation in the context of the bifurcation of the α process and (Johari) ß process found in many glass-forming materials to occur near Tc. Our analysis lays the foundation for a study of the jump-length and waiting-time distributions, their temperature and chain-length dependencies, and the modeling of the monomer dynamics by a CTRW approach in the companion paper [J. Helfferich et al., Phys. Rev. E 89, 042604 (2014)].

Continuous-time random-walk approach to supercooled liquids. II. Mean-square displacements in polymer melts.

The continuous-time random walk (CTRW) describes the single-particle dynamics as a series of jumps separated by random waiting times. This description is applied to analyze trajectories from molecular dynamics (MD) simulations of a supercooled polymer melt. Based on the algorithm presented by Helfferich et al. [Phys. Rev. E 89, 042603 (2014)], we detect jump events of the monomers. As a function of temperature and chain length, we examine key distributions of the CTRW: the jump-length distribution (JLD), the waiting-time distribution (WTD), and the persistence-time distribution (PTD), i.e., the distribution of waiting times for the first jump. For the equilibrium (polymer) liquid under consideration, we verify that the PTD is determined by the WTD. For the mean-square displacement (MSD) of a monomer, the results for the CTRW model are compared with the underlying MD data. The MD data exhibit two regimes of subdiffusive behavior, one for the early α process and another at later times due to chain connectivity. By contrast, the analytical solution of the CTRW yields diffusive behavior for the MSD at all times. Empirically, we can account for the effect of chain connectivity in Monte Carlo simulations of the CTRW. The results of these simulations are then in good agreement with the MD data in the connectivity-dominated regime, but not in the early α regime where they systematically underestimate the MSD from the MD.

Simulating dynamic crossover behavior of semiflexible linear polymers in solution and in the melt.

We present a molecular dynamics study of the dynamic scaling behavior of linear polymers in solution and in the melt when their character changes from fully flexible to semiflexible. The stiffness of the chains is determined by a bending potential. It is shown that the relaxation times tau(p) characterizing the internal dynamics of the polymer chains as well as the mean square mode amplitudes exhibit a clear crossover from Rouse to bending modes with increasing mode number p. For small mode numbers p the well-known p(-2) Rouse behavior is observed, whereas large mode numbers exhibit the p(-4) scaling, typical of the bending modes of semiflexible chains. We study the extension and the onset of the region where the crossover from p(-2) to p(-4) behavior occurs. With increasing stiffness of the chains we observe a shift of the crossover domain to smaller p-values. We also investigate the effect of chain stiffness on the monomer dynamics, based on their mean square displacements. Finally, we compare our results to previous simulations, where the scaling behavior of semiflexible chains was studied and which were restricted to a smaller range of persistence lengths l(p) and p values.

Spacers' role in the dynamics of hyperbranched polymers.

We investigate hyperbranched polymers (HBPs) and highlight the relation between their architecture and their viscoelastic behavior, while paying special attention to the role of the chainlike spacer segments between branching points. For this we study the dynamics of HBP in solution, based on the generalized Gaussian structure formalism, an extension of the Rouse model, which disregards hydrodynamical and excluded volume effects. For HBP the dynamical effects display, beside the obvious contributions of localized modes on the spacers, also remarkable features, as we highlight based on the exact renormalization procedure recently developed by us in J. Chem. Phys. 123, 034907 (2005). We exemplify these features by analyzing the dynamics of randomly linked star polymers and study the impact both of the length and of the spacers' mobility on the normal modes' spectra. We compute these modes both by numerical diagonalization and also by employing our renormalization procedure; the excellent agreement between these methods allows us to extend the range of investigations to very large HBP.

Analytically solvable model in fractional kinetic theory.

In this article we give a general prescription for incorporating memory effects in phase space kinetic equation, and consider in particular the generalized "fractional" relaxation time model equation. We solve this for small-signal charge carriers undergoing scattering, trapping, and detrapping in a time-of-flight experimental arrangement in two ways: (i) approximately via the Chapman-Enskog scheme for the weak gradient, hydrodynamic regime, from which the fractional form of Fick's law and diffusion equation follow; and (ii) exactly, without any limitations on gradients. The latter yields complete and exact expressions in terms of generalized Mittag-Lefler functions for experimentally observable quantities. These expressions enable us to examine in detail the transition from the nonhydrodynamic stage to the hydrodynamic regime, and thereby establish the limits of validity of Fick's law and the corresponding fractional diffusion equation.

Dynamics of end-linked star-polymer structures.

In this work we focus on the dynamics of macromolecular networks formed by end-linking identical polymer stars. The resulting macromolecular network can then be viewed as consisting of spacers which connect branching points (the cores of the stars). We succeed in analyzing exactly, in the framework of the generalized Gaussian model, the eigenvalue spectrum of such networks. As applications we focus on several topologies, such as regular networks and dendrimers; furthermore, we compare the results to those found for regular hyperbranched structures. In so doing, we also consider situations in which the beads of the cores differ from the beads of the spacers. The analytical procedure which we use involves an exact real-space renormalization, which allows to relate the star network to a (much simpler) network, in which each star is reduced to its core. It turns out that the eigenvalue spectrum of the star-polymer structure consists of two parts: one follows in terms of polynomial equations from the relaxation spectrum of the corresponding renormalized structure, while the second part involves the motion of the spacer chains themselves. Finally, we show exemplarily the situation for copolymeric dendrimers, calculate their spectra, and from them their storage and the loss moduli.

Dynamical scaling behavior of percolation clusters in scale-free networks.

In this work we investigate the spectra of Laplacian matrices that determine many dynamic properties of scale-free networks below and at the percolation threshold. We use a replica formalism to develop analytically, based on an integral equation, a systematic way to determine the ensemble averaged eigenvalue spectrum for a general type of treelike networks. Close to the percolation threshold we find characteristic scaling functions for the density of states rho(lambda) of scale-free networks. rho(lambda) shows characteristic power laws rho (lambda) approximately lambda (alpha(1) ) or rho (lambda) approximately lambda (d(2) ) for small lambda, where alpha(1) holds below and alpha(2) at the percolation threshold. In the range where the spectra are accessible from a numerical diagonalization procedure the two methods lead to very similar results.

Dynamics of randomly branched polymers: configuration averages and solvable models.

Treating the relaxation dynamics of an ensemble of random hyperbranched macromolecules in dilute solution represents a challenge even in the framework of Rouse-type approaches, which focus on generalized Gaussian structures (GGSs). The problem is that one has to average over a large class of realizations of molecular structures, and that each molecule undergoes its own dynamics. We show that a replica formalism allows to develop analytically, based on an integral equation, a systematic way to determine the ensemble averaged eigenvalue spectrum. Interestingly, for a specific probability distribution of the spring strengths of the GGSs, the integral equation takes a particularly simple form. Given that several dynamical observables, such as the mechanical moduli G'(omega) and G"(omega), as well as the averaged monomer displacement are relatively simple functions of the eigenvalues, we can use the obtained spectra to compute the corresponding averaged dynamical forms. Comparing the results obtained from this approach and from extensive diagonalizations of hyperbranched GGSs we find a very good agreement.

Dynamics of Vicsek fractals, models for hyperbranched polymers.

We consider the dynamics of Vicsek fractals of arbitrary connectivity, models for hyperbranched polymers. Their basic dynamical properties depend on their eigenvalue spectra, which can be determined iteratively. This paves the way for theoretical studies to very high precision for regular, finite, arbitrarily large hyperbranched structures.

Trapping of random walks on small-world networks.

We investigate the trapping of random walkers on small-world networks (SWN's), irregular graphs. We derive bounds for the survival probability Phi(SWN)(n) and display its analysis through cumulant expansions. Computer simulations are performed for large SWNs. We show that in the limit of infinite sizes, trapping on SWNs is equivalent to trapping on a certain class of random trees, which are grown during the random walk.

Do strange kinetics imply unusual thermodynamics?

We introduce a fractional Fokker-Planck equation (FFPE) for Lévy flights in the presence of an external field. The equation is derived within the framework of the subordination of random processes which leads to Lévy flights. It is shown that the coexistence of anomalous transport and a potential displays a regular exponential relaxation toward the Boltzmann equilibrium distribution. The properties of the Lévy-flight FFPE derived here are compared with earlier findings for a subdiffusive FFPE. The latter is characterized by a nonexponential Mittag-Leffler relaxation to the Boltzmann distribution. In both cases, which describe strange kinetics, the Boltzmann equilibrium is reached, and modifications of the Boltzmann thermodynamics are not required.

Directed particle diffusion under "burnt bridges" conditions.

We study random walks on a one-dimensional lattice that contains weak connections, so-called "bridges." Each time the walker crosses the bridge from the left or attempts to cross it from the right, the bridge may be destroyed with probability p; this restricts the particle's motion and directs it. Our model, which incorporates asymmetric aspects in an otherwise symmetric hopping mechanism, is very akin to "Brownian ratchets" and to front propagation in autocatalytic A+B-->2A reactions. The analysis of the model and Monte Carlo simulations show that for large p the velocity of the directed motion is extremely sensitive to the distribution of bridges, whereas for small p the velocity can be understood based on a mean-field analysis. The single-particle model advanced by us here allows an almost quantitative understanding of the front's position in the A+B-->2A many-particle reaction.

Disorder and plasticity in the fragmentation of coatings.

Using a one-dimensional model that takes into account ideal plasticity of the surface layer, we investigate the fragmentation of thin coatings under uniaxial tension. The coating is modeled as a chain of plastically deforming elements that are connected via leaf springs to a uniformly stretched substrate. Each coating element can only withstand a maximum elongation, which is randomly distributed. From simulations of the fragmentation process we find that the average crack spacing scales with applied strain epsilon, i.e., proportional to epsilon(-kappa). Simulations and analytical arguments show that the scaling exponent kappa depends on the disorder parameters of the model.

Target problem on small-world networks.

In this work we focus on reactions on small-world networks (SWN's), disordered graphs of much recent interest. We study the target problem, since it allows an exact solution on regular lattices. On SWN's we find that the decay of the targets (for which we extend the formalism to disordered lattices) is again related to S(n), the mean number of distinct sites visited in n steps, although the S(n) vs n dependence changes here drastically in going from regular linear chains to their SWN.

Polymer dynamics in time-dependent Matheron-de Marsily flows: an exactly solvable model.

We introduce a model of random layered media, extending the Matheron-de Marsily model: Here we allow for the flows to change in time. For such layered structures, we solve exactly the equations of motion for single particles and also for polymers modelled as Rouse chains. The results show a rich variety of dynamical patterns.

Small-world networks: links with long-tailed distributions

Small-world networks (SWN), obtained by randomly adding to a regular structure additional links (AL), are of current interest. In this paper we explore (based on physical models) a new variant of SWN, in which the probability of realizing an AL depends on the chemical distance between the connected sites. We assume a power-law probability distribution and study random walkers on the network, focusing especially on their probability of being at the origin. We connect the results to Levy flights, which follow from a mean-field variant of our model.

Front propagation in one-dimensional autocatalytic reactions: the breakdown of the classical picture at small particle concentrations

The autocatalytic scheme A+B-->2A in a discrete particle system is studied in one dimension via Monte Carlo simulations. We find considerable differences in the results for the front velocities and front forms compared to the classical, continuous picture, which is only valid in the limit of very small reaction probabilities p. Interestingly, we also obtain front propagation velocities fairly below the classical minimal velocity.

Relaxation properties of small-world networks

Recently, Watts and Strogatz introduced the so-called small-world networks in order to describe systems that combine simultaneously properties of regular and random lattices. In this work we study diffusion processes defined on such structures by considering explicitly the probability for a random walker to be present at the origin. The results are intermediate between the corresponding ones for fractals and Cayley trees.