We investigate the Rouse dynamics of a flexible ring polymer with a prime knot. Within a Monte Carlo approach, we locate the knot, follow its diffusion, and observe the fluctuations of its length. We characterise a topological time scale, and show that it is related to a self-reptation of the knotted region. The associated dynamical exponent, $z_T=2.32\pm.1$, can be related to that of the equilibrium knot length distribution and determines the behaviour of several dynamical quantities.
We give a lower bound on the diffusion coefficient of a polymer chain in an entanglement network with kinematic disorder, which is obtained from an exact calculation in a modified Rubinstein-Duke lattice gas model with periodic boundary conditions. In the limit of infinite chain length we show the diffusive motion of the polymer to be slowed down by kinematic disorder by the same factor as for a single particle in a random barrier model.
We analyze the motion of individual beads of a polymer chain using a discrete version of De Gennes' reptation model that describes the motion of a polymer through an ordered lattice of obstacles. The motion within the tube can be evaluated rigorously, tube renewal is taken into account in an approximation motivated by random walk theory. We find microstructure effects to be present for remarkably large times and long chains, affecting essentially all present day computer experiments. The various asymptotic power laws, commonly considered as typical for reptation, hold only for extremely long c…
The effect of ambient disorders and sequence heterogeneities on the reptation of a long polymer is studied with the aid of a disordered tube model. The dynamics of a random heteropolymer is found to be much slower than that of a homopolymer due to collective pinning effects. The asymptotic properties belong to the universality class of a directed path in (1+1)-dimensional random media.
We investigate the nonequilibrium tube length fluctuations during the relaxation of an initially stretched, entangled polymer chain. The time-dependent variance $σ^2$ of the tube length follows in the early-time regime a simple universal power law $σ^2 = A \sqrt{t}$ originating in the diffusive motion of the polymer segments. The amplitude $A$ is calculated analytically both from standard reptation theory and from an exactly solvable lattice gas model for reptation and its dependence on the initial and equilibrium tube length respectively is discussed. The non-universality suggests the measure…
We compare Monte Carlo simulations of knotted and unknotted polymers whose ends are connected to two parallel walls. The force $f$ exerted on the polymer is measured as a function of the separation $R$ between the walls. For unknotted polymers of several monomer numbers $N$, the product $fN^ν$ is a simple function of $R/N^ν$, where $ν\simeq 0.59$. By contrast, knotted polymers exhibit strong finite size effects which can be interpreted in terms of a new length scale related to the size of the knot. Based on this interpretation, we conclude that the number of monomers forming the knot scales as…
We study the motion of long polymers (eg DNA) in a gel under the influence of an external force acting locally on small segments of the polymer. In particular, we examine the dependence of the drift velocity on the position where the force acts and the length of the polymer. As an application, we discuss the possibility of gel magnetophoresis - the size-separation of long polymers by the attachment of a magnetic bead at an arbitrary position along the length of the polymer. We show that there is a regime where the separation of such polymers with this `random-position beading' is possible.
Reptation theory has been highly successful in explaining the unusual material properties of entangled polymer solutions. It reduces the complex many-body dynamics to a single-polymer description where each polymer is envisaged to be confined to a tube through which it moves in a snake-like fashion. For flexible polymers, reptation theory has been amply confirmed by both experiments and simulations. In contrast, for semiflexible polymers experimental and numerical tests are either limited to the onset of reptation, or were performed for tracer polymers in a fixed, static matrix. Here we report…
We study knotted polymers in equilibrium with an array of obstacles which models confinement in a gel or immersion in a melt. We find a crossover in both the geometrical and the topological behavior of the polymer. When the polymers' radius of gyration, $R_G$, and that of the region containing the knot, $R_{G,k}$, are small compared to the distance b between the obstacles, the knot is weakly localised and $R_G$ scales as in a good solvent with an amplitude that depends on knot type. In an intermediate regime where $R_G > b > R_{G,k}$, the geometry of the polymer becomes branched. When $R_{G,k}…
A simple one-dimensional model is constructed for polymer motion. It exhibits the crossover from reptation to Rouse dynamics through gradually allowing hernia creation and annihilation. The model is treated by the density matrix technique which permits an accurate finite-size-scaling analysis of the behavior of long polymers.
Polymer entanglements lead to complicated topological constraints and interactions between neighbouring chains in a dense solution or melt. Entanglements can be treated in a mean field approach, within the famous reptation model, since they effectively confine each individual chain in a tube-like geometry. In polymer networks, due to crosslinks preventing the reptation constraint release, entanglements acquire a different topological meaning and have a much stronger effect on the resulting mechanical response. We apply the classical ideas of reptation dynamics to calculate the effective rubber…
The cage model for polymer reptation is extended to simulate DC electrophoresis. The drift velocity v of a polymer with length L in an electric field with strength E shows three different regions: if the strength of field is small, the drift velocity scales as E/L; for slightly larger strengths, it scales as E^2, independent of length; for high fields, but still E much smaller than 1, the drift velocity decreases exponentially to zero. The behaviour of the first two regions are in agreement with earlier reports on simulations of the Duke-Rubinstein model and with experimental work on DNA polym…
To establish a standard for the distinction of reptation from other modes of polymer diffusion, we analytically and numerically study the displacement of the central bead of a chain diffusing through an ordered obstacle array for times $t < O(N^2)$. Our theory and simulations agree quantitatively and show that the second moment approaches the $t^{1/4}$ often viewed as signature of reptation only after a very long transient and only for long chains (N > 100). Our analytically solvable model furthermore predicts a very short transient for the fourth moment. This is verified by computer experimen…
Two types of average structures of a single knotted ring polymer are studied by Brownian dynamics simulations. For a ring polymer with N segments, its structure is represented by a 3N -dimensional conformation vector consisting of the Cartesian coordinates of the segment positions relative to the center of mass of the ring polymer. The average structure is given by the average conformation vector, which is self-consistently defined as the average of the conformation vectors obtained from a simulation each of which is rotated to minimize its distance from the average conformation vector. From e…
The statistical mechanics of a long knotted collapsed polymer is determined by a free-energy with a knot-dependent subleading term, which is linked to the length of the shortest polymer that can hold such knot. The only other parameter depending on the knot kind is an amplitude such that relative probabilities of knots do not vary with the temperature $T$, in the limit of long chains. We arrive at this conclusion by simulating interacting self-avoiding rings at low $T$ on the cubic lattice, both with unrestricted topology and with setups where the globule is divided by a slip link in two loops…
Inspired by how certain proteins "sense" knots and entanglements in DNA molecules, here we ask if there exist local geometric features that may be used as a read-out of the underlying topology of generic polymers. We perform molecular simulations of knotted and linked semiflexbile polymers and study four geometric measures to predict topological entanglements: local curvature, local density, local 1D writhe and non-local 3D writhe. We discover that local curvature is a poor predictor of entanglements. In contrast, segments with maximum local density or writhe correlate as much as 90% of the ti…
We investigate the Rubinstein-Duke model for polymer reptation by means of density-matrix renormalization group techniques both in absence and presence of a driving field. In the former case the renewal time τand the diffusion coefficient D are calculated for chains up to N=150 reptons and their scaling behavior in N is analyzed. Both quantities scale as powers of N: $τ\sim N^z$ and $D \sim 1/N^x$ with the asymptotic exponents z=3 and x=2, in agreement with the reptation theory. For an intermediate range of lengths, however, the data are well-fitted by some effective exponents whose values are…
By performing Monte Carlo sampling of $N$-steps self-avoiding polygons embedded on different Bravais lattices we explore the robustness of universality in the entropic, metric and geometrical properties of knotted polymer rings. In particular, by simulating polygons with $N$ up to $10^5$ we furnish a sharp estimate of the asymptotic values of the knot probability ratios and show their independence on the lattice type. This universal feature was previously suggested although with different estimates of the asymptotic values. In addition we show that the scaling behavior of the mean squared radi…
The cage model for polymer reptation, proposed by Evans and Edwards, and its recent extension to model DNA electrophoresis, are studied by numerically exact computation of the drift velocities for polymers with a length L of up to 15 monomers. The computations show the Nernst-Einstein regime (v ~ E) followed by a regime where the velocity decreases exponentially with the applied electric field strength. In agreement with de Gennes' reptation arguments, we find that asymptotically for large polymers the diffusion coefficient D decreases quadratically with polymer length; for the cage model, the…
The competition between reptation and Rouse Dynamics is incorporated in the Rubinstein-Duke model for polymer motion by extending it with sideways motions, which cross barriers and create or annihilate hernias. Using the Density-Matrix Renormalization-Group Method as solver of the Master Equation, the renewal time and the diffusion coefficient are calculated as function of the length of the chain and the strength of the sideways motion. These new types of moves have a strong and delicate influence on the asymptotic behavior of long polymers. The effects are analyzed as function of the chain le…
We consider an arbitrarily charged polymer driven by a weak field through a gel according to the rules of the Rubinstein-Duke model. The probability distribution in the stationary state is related to that of the model in which only the head is charged. Thereby drift velocity, diffusion constant and orientation of any charged polymers are expressed in terms of those of the central model. Mapping the problem on a random walk of a tagged particle along a one-dimenional chain, leads to a unified scaling expression for the local orientation. It provides also an elucidation of the role of correction…
We introduce a two-dimensional lattice model for the description of knotted polymer rings. A polymer configuration is modeled by a closed polygon drawn on the square diagonal lattice, with possible crossings describing pairs of strands of polymer passing on top of each other. Each polygon configuration can be viewed as the two- dimensional projection of a particular knot. We study numerically the statistics of large polygons with a fixed knot type, using a generalization of the BFACF algorithm for self-avoiding walks. This new algorithm incorporates both the displacement of crossings and the t…
The effects of entanglement in solutions and melts of unknotted ring polymers have been addressed by several theoretical and numerical studies. The system properties have been typically profiled as a function of ring contour length at fixed solution density. Here, we use a different approach to investigate numerically the equilibrium and kinetic properties of solutions of model ring polymers. Specifically, the ring contour length is maintained fixed, while the interplay of inter- and intra-chain entanglement is modulated by varying both solution density (from infinite dilution up to \approx 40…
Several nontrivial properties are shown for the mean square radius of gyration $R_K^2$ of ring polymers with a fixed knot type K. Through computer simulation, we discuss both finite-size and asymptotic behaviors of the gyration radius under the topological constraint for self-avoiding polygons consisting of N cylindrical segments with radius r. We find that the average size of ring polymers with a knot K can be much larger than that of no topological constraint. The effective expansion due to the topological constraint depends strongly on the parameter r which is related to the excluded volume…
The two-dimensional cage model for polymer motion is discussed with an emphasis on the effect of sideways motions, which cross the barriers imposed by the lattice. Using the Density Matrix Method as a solver of the Master Equation, the renewal time and the diffusion coefficient are calculated as a function of the strength of the barrier crossings. A strong crossover influence of the barrier crossings is found and it is analyzed in terms of effective exponents for a given chain length. The crossover scaling functions and the crossover scaling exponents are calculated.
The thermal properties of coarse grained knotted polymers containing two kinds of monomers $A$ and $B$ fluctuating in a solution are investigated on a simple cubic lattice using the Wang-Landau MC algorithm. These knots have a more complex phase diagram than knots formed by homopolymers, including the possible presence of metastable states. Two different setups are considered: i) charged block copolymers in a ion solution and ii) neutral copolymers with the $A$ monomers above and the $B$ monomers below the theta point. A precise interpretation of the peaks observed in the plots of the specific…
Polymer dynamics at large fields in Rubinstein-Duke repton model is investigated theoretically. Simple diagrammatic approach and analogy with asymmetric simple exclusion models are used to analyze the reptation dynamics of polymers. It is found that for polyelectrolytes the drift velocity decreases exponentially as a function of the external field with an exponent depending on polymer size and parity, while for polyampholytes the drift velocity is independent of polymer chain size. However, for polymers, consisting of charged and neutral blocks, the drift velocity approaches the constant limit…
The correlations in the motion of reptating polymers in their melt are investigated by means of kinetic Monte Carlo simulations of the three dimensional slithering snake version of the bond-fluctuation model. Surprisingly, the slithering snake dynamics becomes inconsistent with classical reptation predictions at high chain overlap (either chain length $N$ or volume fraction $ϕ$) where the relaxation times increase much faster than expected. This is due to the anomalous curvilinear diffusion in a finite time window whose upper bound $τ_+$ is set by the chain end density $ϕ/N$. Density fluctuati…
We compare the Rubinstein-Duke model for reptation to a model where the boundary dynamics is modified by calculating the viscosity of polymer melts. The question is investigated whether the viscosity is determined by details of the dynamics of the polymer ends or by the stretching of the polymer. To this end the dependence of the viscosity on the particle density of the lattice gas models which can be identified by the stretching is determined. We show that the influence of the stretching of the polymer on the absolute value of the viscosity in the scaling limit of of very long chains is much …
It has been recently shown that the phase space trajectories for the anomalous dynamics of a tagged monomer of a polymer --- for single polymeric systems such as phantom Rouse, self-avoiding Rouse, Zimm, reptation, and translocation through a narrow pore in a membrane; as well as for many-polymeric system such as polymer melts in the entangled regime --- is robustly described by the Generalized Langevin Equation (GLE). Here I show that the probability distribution of phase space trajectories for all these classical anomalous dynamics for single polymers is that of a fractional Brownian motion …
In entangled polymer systems, there are several characteristic time scales, such as the entanglement time and the disengagement time. In molecular simulations, the longest relaxation time (the disengagement time) can be determined by the mean square displacement (MSD) of a segment or by the shear relaxation modulus. Here, we propose the relative fluctuation analysis method, which is originally developed for characterizing large fluctuations, to determine the longest relaxation time from the center of mass trajectories of polymer chains (the time-averaged MSDs). Applying the method to simulatio…
Numerical studies of the average size of trivially knotted polymer loops with no excluded volume are undertaken. Topology is identified by Alexander and Vassiliev degree 2 invariants. Probability of a trivial knot, average gyration radius, and probability density distributions as functions of gyration radius are generated for loops of up to N=3000 segments. Gyration radii of trivially knotted loops are found to follow a power law similar to that of self avoiding walks consistent with earlier theoretical predictions.
There have been increasing reports that the diffusion coefficient of macromolecules depends on time and fluctuates randomly. Here, a novel method to elucidate the fluctuating diffusivity from trajectory data is developed. The time-averaged mean square displacement (MSD), a common tool in single-particle-tracking (SPT) experiments, is generalized into a second order tensor, with which information on both magnitude fluctuations and orientational fluctuations of the diffusivity can be clearly detected. This new method is utilized to analyze the center-of-mass motion of four polymer models, the Ro…
We analyze the Rubinstein-Duke model for polymer reptation by means of density matrix renormalization techniques. We find a crossover behavior for a series of quantities as function of the polymer length. The crossover length may become very large if the mobility of end groups is small compared to that of the internal reptons. Our results offer an explanation to a controversy between theory, experiments and simulations on the leading and subleading scaling behavior of the polymer renewal time and diffusion constant.
We study the dynamics of a single chain polymer confined to a two dimensional cell. We introduce a kinetically constrained lattice gas model that preserves the connectivity of the chain, and we use this kinetically constrained model to study the dynamics of the polymer at varying densities through Monte Carlo simulations. Even at densities close to the fully-packed configuration, we find that the monomers comprising the chain manage to diffuse around the box with a root mean square displacement of the order of the box dimensions over time scales for which the overall geometry of the polymer is…
Semiflexible polymer models are widely used as a paradigm to understand structural phases in biomolecules including folding of proteins. Since stable knots are not so common in real proteins, the existence of stable knots in semiflexible polymers has not been explored much. Here, via extensive replica exchange Monte Carlo simulation we investigate the same for a bead-stick and a bead-spring homopolymer model that covers the whole range from flexible to stiff. We establish the fact that the presence of stable knotted phases in the phase diagram is dependent on the ratio $r_b/r_{\rm{min}}$ where…
We study the translocation process of a polymer in the absence of external fields for various pore diameters $b$ and membrane thickness $L$. The polymer performs Rouse and reptation dynamics. The mean translocation time $<τ_t>$ that the polymer needs to escape from a cell, and the mean dwell time $<τ_d>$ that the polymer spends in the pore during the translocation process, obey scaling relations in terms of the polymer length $N$, $L$ and $b/R_g$, where $R_g$ is the radius of gyration for the polymer. We explain these relations using simple arguments based on polymer dynamics and the equilibri…
Using a combination of the replica-exchange Monte Carlo algorithm and the multicanonical method, we investigate the influence of bending stiffness on the conformational phases of a bead-stick homopolymer model and present the pseudo-phase diagram for the complete range of semi-flexible polymers, from flexible to stiff. Although a simple model, we observe a rich variety of conformational phases, reminiscent of conformations observed for synthetic polymers or biopolymers. Changing the internal bending stiffness, the model exhibits different pseudo phases like bent, hairpin or toroidal. In partic…
A compressed knotted ring polymer in a confining cavity is modelled by a knotted lattice polygon confined in a cube in ${\mathbb Z}^3$. The GAS algorithm [17] is used to sample lattice polygons of fixed knot type in a confining cube and to estimate the free energy of confined lattice knots. Lattice polygons of knot types the unknot, the trefoil knot, and the figure eight knot, are sampled and the free energies are estimated as functions of the concentration of monomers in the confining cube. The data show that the free energy is a function of knot type at low concentrations, and (mean-field) F…
Any first course on polymer physics teaches that the dynamics of a tagged monomer of a polymer is anomalously subdiffusive, i.e., the mean-square displacement of a tagged monomer increases as $t^α$ for some $α<1$ until the terminal relaxation time $τ$ of the polymer. Beyond time $τ$ the motion of the tagged monomer becomes diffusive. Classical examples of anomalous dynamics in polymer physics are single polymeric systems, such as phantom Rouse, self-avoiding Rouse, self-avoiding Zimm, reptation, translocation through a narrow pore in a membrane, and many-polymeric systems such as polymer melts…
Using a lattice model of polymers in a tube, we define one way to characterise different configurations of a given knot as either "local" or "non-local" and, for several ring polymer models, we provide both theoretical and numerical evidence that, at equilibrium, the non-local configurations are more likely than the local ones. These characterisations are based on a standard approach for measuring the "size" of a knot within a knotted polymer chain. The method involves associating knot-types to subarcs of the chain, and then identifying a knotted subarc with minimal arclength; this arclength i…
In frameworks of the scaling theory of phase transitions and critical phenomena the quantitative dependence of macroscopic properties on nanostructural parameters in a polymeric material is revealed. The draw ratios at neck and at break are referred to the macroscopic properties. The structure is characterized by an average thickness of amorphous layers in isotropic melt-crystallized linear high density polyethylene which is chosen as an example. The square of the neck draw ratio is equal to the product of the square of the draw ratio at break and the chain ends collision probability. This pro…
Linear polymers are represented as chains of hopping reptons and their motion is described as a stochastic process on a lattice. This admittedly crude approximation still catches essential physics of polymer motion, i.e. the universal properties as function of polymer length. More than the static properties, the dynamics depends on the rules of motion. Small changes in the hopping probabilities can result in different universal behavior. In particular the cross-over between Rouse dynamics and reptation is controlled by the types and strength of the hoppings that are allowed. The properties are…
A veritable zoo of different knots is seen in the ensemble of looped polymer chains, whether created computationally or observed in vitro. At short loop lengths, the spectrum of knots is dominated by the trivial knot (unknot). The fractional abundance of this topological state in the ensemble of all conformations of the loop of $N$ segments follows a decaying exponential form, $ \sim \exp (-N/N_0)$, where $N_0$ marks the crossover from a mostly unknotted (ie topologically simple) to a mostly knotted (ie topologically complex) ensemble. In the present work we use computational simulation to loo…
We use Brownian dynamics simulations and advanced topological profiling methods to characterize the out-of-equilibrium evolution of self-entanglement in linear polymers confined into nano-channels and under periodic compression. We distinguish two main forms of entanglement, geometrical and topological. The latter is measured by the number of (essential) crossings of the physical knot detected after a suitable bridging of the chain termini. The former is instead measured as the average number of times a linear chain appears to cross itself when viewed under all projections, and is irrespective…
We construct a tractable model to describe the rate at which a knotted polymer is ejected from a spherical capsid via a small pore. Knots are too large to fit through the pore and must reptate to the end of the polymer for ejection to occur. The reptation of knots is described by symmetric exclusion on the line, with the internal capsid pressure represented by an additional biased particle that drives knots to the end of the chain. We compute the exact ejection speed for a finite number of knots L and find that it scales as 1/L. We also construct a continuum theory for many knots that matches …
The interplay of geometrical and topological entanglement in semiflexible knotted polymer rings confined inside a spherical cavity is investigated using advanced numerical methods. By using stringent and robust algorithms for locating knots, we characterize how the knot length lk depends on the ring contour length, Lc and the radius of the confining sphere, Rc . In the no- and strong- confinement cases we observe weak knot localization and complete knot delocalization, respectively. We show that the complex interplay of lk, Lc and Rc that seamlessly bridges these two limits can be encompassed …
We develop a segment-scale, force-based theory for the breakdown of the unentangled Rouse model and subsequent emergence of isotropic mesoscopic localization and entropic elasticity in chain polymer liquids in the absence of ergodicity-restoring anisotropic reptation motion. The theory is formulated in terms of a conformational N-dynamic-order-parameter Generalized Langevin Equation approach. It is implemented using a field-theoretic Gaussian thread model of polymer structure and closed in a universal manner at the level of the chain dynamic second moment matrix. The physical idea is that the …
In this work a new strategy is proposed in order to build analytic and microscopic models of fluctuating polymer rings subjected to topological constraints. The topological invariants used to fix these constraints belong to a wide class of the so-called numerical topological invariants. For each invariant it is possible to derive a field theory that describes the statistical behavior of knotted and linked polymer rings following a straightforward algorithm. The treatment is not limited to the partition function of the system, but it allows also to express the expectation values of general obse…
We give two different, statistically consistent definitions of the length l of a prime knot tied into a polymer ring. In the good solvent regime the polymer is modelled by a self avoiding polygon of N steps on cubic lattice and l is the number of steps over which the knot ``spreads'' in a given configuration. An analysis of extensive Monte Carlo data in equilibrium shows that the probability distribution of l as a function of N obeys a scaling of the form p(l,N) ~ l^(-c) f(l/N^D), with c ~ 1.25 and D ~ 1. Both D and c could be independent of knot type. As a consequence, the knot is weakly loca…
