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 behaviour for short lengths, which changes to the form of semiflexible filaments at intermediate lengths, to finally go back to a Gaussian form for long contour lengths. By performing a Laplace transform of the governing Fokker-Planck equation of the active Brownian particle, we discuss a direct method to derive exact expressions for all the moments of the relevant dynamical variables, in arbitrary dimensions. These are verified via numerical simulations and used to describe interesting qualitative features such as, for example, dynamical crossovers. Finally we discuss the kurtosis of the ABP's position which we compute exactly and show that it can be used to differentiate between active Brownian particles and active Ornstein-Uhlenbeck process.
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.
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…
Directed polymers (strings) and semiflexible polymers (filaments) are one-dimensional objects governed by tension and bending energy, respectively. They undergo unbinding transitions in the presence of a short-range attractive potential. Using transfer matrix methods we establish a duality mapping for filaments and strings between the restricted partition sums in the absence and the presence of a short-range attraction. This allows us to obtain exact results for the critical exponents related to the unbinding transition, the transition point and transition order.
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…
Using a novel theoretical approach, we study the mean first encounter time (MFET) between the two ends of a polymer. Previous approaches used various simplifications that reduced the complexity of the problem, leading, however to incompatible results. We construct here for the first time a general theory that allows us to compute the MFET. The method is based on estimating the mean time for a Brownian particle to reach a narrow domain in the polymer configuration space. In dimension two and three, we find that the MFET depends mainly on the first eigenvalue of the associated Fokker-Planck oper…
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…
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…
We use computer simulations to test a simple idea for mapping between long-time self diffusivities obtained from molecular and Brownian dynamics. The strategy we explore is motivated by the behavior of fluids comprising particles that interact via inverse-power-law pair potentials, which serve as good reference models for dense atomic or colloidal materials. Based on our simulation data, we present an empirical expression that semi-quantitatively describes the "atomic" to "colloidal" diffusivity mapping for inverse-power-law fluids, but also for model complex fluids with considerably softer (s…
We introduce mapping-variable ring polymer molecular dynamics (MV-RPMD), a model dynamics for the direct simulation of multi-electron processes. An extension of the RPMD idea, this method is based on an exact, imaginary time path-integral representation of the quantum Boltzmann operator using continuous Cartesian variables for both electronic states and nuclear degrees of freedom. We demonstrate the accuracy of the MV-RPMD approach in calculations of real-time, thermal correlation functions for a range of two-state single-mode model systems with different coupling strengths and asymmetries. Fu…
We study a Brownian particle passively driven by a field obeying the noisy Burgers equation. We demonstrate that the system exhibits replica symmetry breaking in the path ensemble with the initial position of the particle being fixed. The key step of the proof is that the path ensemble with a modified boundary condition can be exactly mapped to the canonical ensemble of directed polymers.
The Dynamic Density Functional (DDF) theory and standard Brownian dynamics simulations (BDS) are used to study the drifting effects of a colloidal particle in a polymer solution, both for ideal and interacting polymers. The structure of the stationary density distributions and the total induced current are analyzed for different drifting rates. We find good agreement with the BDS, which gives support to the assumptions of the DDF theory. The qualitative aspect of the density distribution are discussed and compared to recent results for driven colloids in one-dimensional channels and to analyti…
The solution of a Caputo time fractional diffusion equation of order $0<α<1$ is expressed in terms of the solution of a corresponding integer order diffusion equation. We demonstrate a linear time mapping between these solutions that allows for accelerated computation of the solution of the fractional order problem. In the context of an $N$-point finite difference time discretisation, the mapping allows for an improvement in time computational complexity from $O\left(N^2\right)$ to $O\left(N^α\right)$, given a precomputation of $O\left(N^{1+α}\ln N\right)$. The mapping is applied successfully …
This work proposes a method for the two-dimensional simulation of Brownian particles in a fluid with restrictions. The method is based on simple numerical rules between two matrices. One of the matrix represent the identification of all particles over which are adapted statistics rules for particles movement, the results are mapped over other matrix which represent the particles positions. The rules for the movement are established by a statistic mechanism allowing assign random or non-random movement direction. The same probably of movement for each direction for each time step is assumed, in…
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.
Recent in vitro experiments with FtsZ polymers show self-organization into different dynamic patterns, including structures reminiscent of the bacterial Z-ring. We model FtsZ polymers as active particles moving along chiral, circular paths by Brownian dynamics simulations and a Boltzmann approach. Our two conceptually different methods point to a generic phase behavior. At intermediate particle densities, we find self-organization into vortex structures including closed rings. Moreover, we show that the dynamics at the onset of pattern formation is described by a generalized complex Ginzburg-L…
We develop coarse-grained force fields for poly (vinyl alcohol) and poly (acrylic acid) oligomers. In both cases, one monomer is mapped onto a coarse-grained bead. The new force fields are designed to match structural properties such as radial distribution functions of various kinds derived by atomistic simulations of these polymers. The mapping is therefore constructed in a way to take into account as much atomistic information as possible. On the technical side, our approach consists of a simplex algorithm which is used to optimize automatically non-bonded parameters as well as bonded parame…
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…
Recently O'Connell introduced an interacting diffusive particle system in order to study a directed polymer model in 1+1 dimensions. The infinitesimal generator of the process is a harmonic transform of the quantum Toda-lattice Hamiltonian by the Whittaker function. As a physical interpretation of this construction, we show that the O'Connell process without drift is realized as a system of mutually killing Brownian motions conditioned that all particles survive forever. When the characteristic length of interaction killing other particles goes to zero, the process is reduced to the noncollidi…
