We demonstrate that size fluctuations close to polymers critical point originate the non-Gaussian diffusion of their center of mass. Static universal exponents $γ$ and $ν$ -- depending on the polymer topology, on the dimension of the embedding space, and on equilibrium phase -- concur to determine the potential divergency of a dynamic response, epitomized by the center of mass kurtosis. Prospects in experiments and stochastic modeling brought about by this result are briefly outlined.
It is well known that path probabilities of Brownian motion correspond to the equilibrium configurational probabilities of flexible Gaussian polymers, while those of active Brownian motion correspond to in-extensible semiflexible polymers. Here we investigate the properties of the equilibrium polymer that corresponds to the trajectories of particles acted on simultaneously by both Brownian as well as active noise. Through this mapping we can see interesting crossovers in mechanical properties of the polymer with changing contour length. The polymer end-to-end distribution exhibits Gaussian beh…
We link the Brownian non-Gaussian diffusion of a polymer center of mass to a microscopic cause: the polymerization/depolymerization phenomenon occurring when the polymer is in contact with a monomer chemostat. The anomalous behavior is triggered by the polymer critical point, separating the dilute and the dense phase in the grand canonical ensemble. In the mean-field limit we establish contact with queuing theory and show that the kurtosis of the polymer center of mass diverges alike a response function when the system becomes critical, a result which holds for general polymer dynamics (Zimm, …
We present an analysis of the mean-field kinetics of Brownian coagulation of droplets and polymers driven by input of monomers which aims to characterize the long time behavior of the cluster size distribution as a function of the inverse fractal dimension, $a$, of the aggregates. We find that two types of long time behavior are possible. For $0\leq a < 1/2$ the size distribution reaches a stationary state with a power law distribution of cluster sizes having exponent 3/2. The amplitude of this stationary state is determined exactly as a function of $a$. For $1/2 < a \leq 1$, the cluster size …
Recent theoretical modeling offers a unified picture for the description of stochastic processes characterized by a crossover from anomalous to normal behavior. This is particularly welcome, as a growing number of experiments suggest the crossover to be a common feature shared by many systems: in some cases the anomalous part of the dynamics amounts to a Brownian yet non-Gaussian diffusion; more generally, both the diffusion exponent and the distribution may deviate from normal behavior in the initial part of the process. Since proposed theories work at a mesoscopic scale invoking the subordin…
We consider two complementary polymer strands of length $L$ attached by a common end monomer. The two strands bind through complementary monomers and at low temperatures form a double stranded conformation (zipping), while at high temperature they dissociate (unzipping). This is a simple model of DNA (or RNA) hairpin formation. Here we investigate the dynamics of the strands at the equilibrium critical temperature $T=T_c$ using Monte Carlo Rouse dynamics. We find that the dynamics is anomalous, with a characteristic time scaling as $τ\sim L^{2.26(2)}$, exceeding the Rouse time $\sim L^{2.18}$.…
A narrow Gaussian excluded volume potential, which tends to a delta-function repulsive potential in the limit of a width parameter d* going to zero, has been used to examine the universal consequences of excluded volume interactions on the equilibrium and linear viscoelastic properties of dilute polymer solutions. Brownian dynamics simulations data, acquired for chains of finite length, has been extrapolated to the limit of infinite chain length to obtain model independent predictions. The success of the method in predicting well known aspects of static solution properties suggests that it can…
Quantitatively understanding of the dynamics of an active Brownian particle (ABP) interacting with a viscoelastic polymer environment is a scientific challenge. It is intimately related to several interdisciplinary topics such as the microrheology of active colloids in a polymer matrix and the athermal dynamics of the in vivo chromosome or cytoskeletal networks. Based on Langevin dynamics simulation and analytic theory, here we explore such a viscoelastic active system in depth using a star polymer of functionality $f$ with the center cross-linker particle being ABP. We observe that the ABP cr…
We have calculated the probability distribution function G(R,L|R',0) of the end-to-end vector R-R' and the mean-square end-to-end distance (R-R')^2 of a Gaussian polymer chain embedded on a sphere S^(D-1) in D dimensions and on a cylinder, a cone and a curved torus in 3-D. We showed that: surface curvature induces a geometrical localization area; at short length the polymer is locally "flat" and (R-R')^2 = L l in all cases; at large scales, (R-R')^2 is constant for the sphere, it is linear in L for the cylinder and reaches different constant values for the torus. The cone vertex induces (funct…
The conformational and dynamical properties of active self-propelled filaments/polymers are investigated in the presence of hydrodynamic interactions by both, Brownian dynamics simulations and analytical theory. Numerically, a discrete linear chain composed of active Brownian particles is considered, analytically, a continuous linear semiflexible polymer with active velocities changing diffusively. The force-free nature of active monomers is accounted for - no Stokeslet fluid flow induced by active forces - and higher order hydrodynamic multipole moments are neglected. The nonequilibrium chara…
We present a comparative study of two computer simulation methods to obtain static and dynamic properties of dilute polymer solutions. The first approach is a recently established hybrid algorithm based upon dissipative coupling between Molecular Dynamics and lattice Boltzmann (LB), while the second is standard Brownian Dynamics (BD) with fluctuating hydrodynamic interactions. Applying these methods to the same physical system (a single polymer chain in a good solvent in thermal equilibrium) allows us to draw a detailed and quantitative comparison in terms of both accuracy and efficiency. It i…
We suggest a governing equation which describes the process of polymer chain translocation through a narrow pore and reconciles the seemingly contradictory features of such dynamics: (i) a Gaussian probability distribution of the translocated number of polymer segments at time $t$ after the process has begun, and (ii) a sub-diffusive increase of the distribution variance $Δ(t)$ with elapsed time, $Δ(t) \propto t^α$. The latter quantity measures the mean-squared number $s$ of polymer segments which have passed through the pore, $Δ(t) = <[s(t)-s(t=0)]^2>$, and is known to grow with an anomalous …
Simulating the static and dynamic properties of semidilute polymer solutions with Brownian dynamics (BD) requires the computation of a large system of polymer chains coupled to one another through excluded-volume and hydrodynamic interactions. In the presence of periodic boundary conditions, long-ranged hydrodynamic interactions are frequently summed with the Ewald summation technique. By performing detailed simulations that shed light on the influence of several tuning parameters involved both in the Ewald summation method, and in the efficient treatment of Brownian forces, we develop a BD al…
We derive an analytical pair potential of mean force for Brownian molecules in the liquid-state. Our approach accounts for many-particle correlations of crowding particles of the liquid, and for diffusive transport across the spatially modulated local density of crowders in the dense environment. Specializing on the limit of equal-size particles, we show that this diffusive transport leads to additional density- and structure-dependent terms in the interaction potential, and to a much stronger attraction (by a factor ~4 at average volume fraction of crowders 0.25) than in the standard depletio…
We investigate a model of chaperone-assisted polymer translocation through a nanopore in a membrane. Translocation is driven by irreversible random sequential absorption of chaperone proteins that bind to the polymer on one side of the membrane. The proteins are larger than the pore and hence the backward motion of the polymer is inhibited. This mechanism rectifies Brownian fluctuations and results in an effective force that drags the polymer in a preferred direction. The translocated polymer undergoes an effective biased random walk and we compute the corresponding diffusion constant. Our met…
In an ensemble of non-interacting Brownian particles, a finite systematic average velocity may temporarily develop, even if it is zero initially. The effect originates from a small nonlinear correction to the dissipative force, causing the equation for the first moment of velocity to couple to moments of higher order. The effect may be relevant when a complex system dissociates in a viscous medium with conservation of momentum.
In this work we study the diffusion of non-interacting overdamped particles, moving on unbiased disordered correlated potentials, subjected to Gaussian white noise. We obtain an exact expression for the diffusion coefficient which allows us to prove that the unbiased diffusion of overdamped particles on a random polymer does not depend on the correlations of the disordered potentials. This universal behavior of the unbiased diffusivity is a direct consequence of the validity of the Einstein relation and the decay of correlations of the random polymer. We test the independence on correlations o…
Three-dimensional Monte Carlo simulations provide a striking confirmation to a recent theoretical prediction: the Brownian non-Gaussian diffusion of critical self-avoiding walks. Although the mean square displacement of the polymer center of mass grows linearly with time (Brownian behavior), the initial probability density function is strongly non-Gaussian and crosses over to Gaussianity only at large time. Full agreement between theory and simulations is achieved without the employment of fitting parameters. We discuss simulation techniques potentially capable of addressing the study of anoma…
We consider the partition function $Z_{\ell}(\vec x,0\vert \vec y,t)$ of $\ell$ non-intersecting continuous directed polymers of length $t$ in dimension $1+1$, in a white noise environment, starting from positions $\vec x$ and terminating at positions $\vec y$. When $\ell=1$, it is well known that for fixed $x$, the field $\log Z_1(x,0\vert y,t)$ solves the Kardar-Parisi-Zhang equation and admits the Brownian motion as a stationary measure. In particular, as $t$ goes to infinity, $Z_1(x,0\vert y,t)/Z_1(x,0\vert 0,t) $ converges to the exponential of a Brownian motion $B(y)$. In this article, w…
Various authors have invoked discretized fractional Brownian (fBm) motion as a model for chain polymers with long range interaction of monomers along the chain. We show that for these, in contrast to the Brownian case, linear forces are acting between all pairs of constituents, attractive for small Hurst index H and mostly repulsive when H is larger than 1/2. In the second part of this paper we extend this study to periodic fBm and related models with a view to ring polymers with long range interactions.
We consider the drift of a polymer chain in a disordered medium, which is caused by a constant force applied to the one end of the polymer, under neglecting the thermal fluctuations. In the lowest order of the perturbation theory we have computed the transversal fluctuations of the centre of mass of the polymer, the transversal and the longitudinal size of the polymer, and the average velocity of the polymer. The corrections to the quantities under consideration, which are due to the interplay between the motion and the quenched forces, are controlled by the driving force and the degree of pol…
We study the translocation of polymers across varying-section channels. Using systematic approximations, we derive a simplified model that reduces the problem of polymer translocation through varying-section channels to that of a point-like particle under the action of an effective potential. Such a model allows us to identify the relevant parameters controlling the polymers dynamics and, in particular, their translocation time. By comparing our analytical results with numerical simulations we show that, under suitable conditions, our model provides reliable predictions of the dynamics of both…
We consider statistics of a planar ideal polymer loop of length $L$ in a large deviation regime, when a gyration radius, $R_g$, is slightly less than the radius of a fully inflated ring, $\frac{L}{2π}$. Specifically, we study analytically and via off-lattice Monte-Carlo simulations relative fluctuations of chain monomers in ensemble of Brownian loops. We have shown that these fluctuations in the regime with fixed large gyration radius are Gaussian with the critical exponent $γ= \frac{1}{2}$. However, if we insert inside the inflated loop the impenetrable disc of radius $R_d=R_g$, the fluctuati…
We present an exact solution for the distribution of sample averaged monomer to monomer distance of ring polymers. For non-interacting and weakly-interacting models these distributions correspond to the distribution of the area under the reflected Bessel bridge and the Bessel excursion respectively, and are shown to be identical in dimension d greater or equal 2. A symmetry of the problem reveals that dimension d and 4 minus d are equivalent, thus the celebrated Airy distribution describing the areal distribution of the one dimensional Brownian excursion describes also a polymer in three dimen…
Vicious Brownian motion is a diffusion scaling limit of Fisher's vicious walk model, which is a system of Brownian particles in one dimension such that if two of them meet they kill each other. We consider the vicious Brownian motion conditioned never to collide with each other, and call it the noncolliding Brownian motion. This conditional diffusion process is equivalent to the eigenvalue process of a Hermitian-matrix-valued Brownian motion studied by Dyson. Recently O'Connell introduced a generalization of the noncolliding Brownian motion by using the eigenfunctions (the Whittaker functions)…
