We use Newtonian and overdamped Langevin dynamics to study long flexible polymers dragged by an external force at a constant velocity $v$. The work $W$ by that force depends on the initial state of the polymer and the details of the process. Jarzynski equality can be used to relate the non-equilibrium work distribution $P(W)$ obtained from repeated experiments to equilibrium free energy difference $ΔF$ between the initial and final states. We use the power law dependence of the geometrical and dynamical characteristics of the polymer on the number of monomers $N$ to suggest the existence of a critical velocity $v_c(N)$, such that for $v<v_c$ the reconstruction of $ΔF$ is an easy task, while for $v$ significantly exceeding $v_c$ it becomes practically impossible. We demonstrate the existence of such $v_c$ analytically for ideal polymer in free space and numerically for a polymer being dragged away from a repulsive wall. Our results suggest that the distribution of the dissipated work $W_{\rm d}=W-ΔF$ in properly scaled variables approaches a limiting shape for large $N$.
When a flexible polymer is sucked into a localized small hole, the chain can initially respond only locally and the sequential nonequilibrium processes follow in line with the propagation of the tensile force along the chain backbone. We analyze this dynamical process by taking the nonuniform stretching of the polymer into account both with and without hydrodynamics interactions. Earlier conjectures on the absorption time are criticized and new formulae are proposed together with time evolutions of relevant dynamical variables.
Recent emerging interest in experiments of single-polymer dynamics urge computational physicists to revive their understandings, particularly in the nonequilibrium context. Here we briefly discuss the currently evolving approaches of investigating the evolution dynamics of homopolymer collapse in computer simulations. Primary focus of these approaches is to understand various dynamic scaling laws related to coarsening and aging during the collapse in space dimension $d=3$, using tools popular in nonequilibrium coarsening dynamics of particle or spin systems. In addition to providing an overvie…
We consider rapid cooling processes in classical, 3-dimensional, purely repulsive binary mixtures in which an initial infinite-temperature (ideal-gas) configuration is instantly quenched to zero temperature. It is found that such systems display two kinds of ordering processes, the type of which can be controlled by tuning the interactions between unlike particles. While strong inter-species repulsion leads to chemical ordering in terms of an unmixing process, weak repulsion gives rise to spontaneous crystallization, maintaining chemical homogeneity. This result indicates the existence of a tr…
We consider forces acting on objects immersed in, or attached to, long fluctuating polymers. The confinement of the polymer by the obstacles results in polymer-mediated forces that can be repulsive (due to loss of entropy) or attractive (if some or all surfaces are covered by adsorbing layers). The strength and sign of the force in general depends on the detailed shape and adsorption properties of the obstacles, but assumes simple universal forms if characteristic length scales associated with the objects are large. This occurs for scale-free shapes (such as a flat plate, straight wire, or con…
In this article we study from a non-perturbative point of view the entanglement of two directed polymers subjected to repulsive interactions given by a Dirac $δ-$function potential. An exact formula of the so-called second moment of the winding angle is derived. This result is used to provide a thorough analysis of entanglement phenomena in the classical system of two polymers subjected to repulsive interactions and related problems. No approximation is made in treating the constraint on the winding angle and the repulsive forces. In particular, we investigate how repulsive forces influence th…
The massive field theory approach in fixed space dimensions $d=3$ is applied to investigate a dilute solution of long-flexible polymer chains in a good solvent between two parallel repulsive walls, two inert walls and for the mixed case of one inert and one repulsive wall. The well known correspondence between the field theoretical $ϕ^4$ O(n)-vector model in the limit $n\to 0$ and the behavior of long-flexible polymer chains in a good solvent is used to calculate the depletion interaction potential and the depletion force up to one-loop order. Our investigations include modification of renorma…
The number of allowed configurations of a polymer is reduced by the presence of a repulsive surface resulting in an entropic force between them. We develop a method to calculate the entropic force, and detailed pressure distribution, for long ideal polymers near a scale-free repulsive surface. For infinite polymers the monomer density is related to the electrostatic potential near a conducting surface of a charge placed at the point where the polymer end is held. Pressure of the polymer on the surface is then related to the charge density distribution in the electrostatic problem. We derive ex…
We show the existence of a nonequilibrium tricritical point induced by a repulsive interaction in one dimensional asymmetric exclusion process. The tricritical point is associated with the particle-hole symmetry breaking introduced by the repulsion. The phase diagram and the crossover in the neighbourhood of the tricritical point for the shock formation at one of the boundaries are determined.
Two-dimensional Raman and hybrid terahertz/Raman spectroscopic techniques provide invaluable insight into molecular structure and dynamics of condensed-phase systems. However, corroborating experimental results with theory is difficult due to the high computational cost of incorporating quantum-mechanical effects in the simulations. Here, we present the equilibrium-nonequilibrium ring-polymer molecular dynamics (RPMD), a practical computational method that can account for nuclear quantum effects on the two-time response function of nonlinear optical spectroscopy. Unlike a recently developed ap…
We investigate the voltage-driven translocation of an inhomogeneously charged polymer through a nanopore by utilizing discrete and continuous stochastic models. As a simplified illustration of the effect of charge distribution on translocation, we consider the translocation of a polymer with a single charged site in the presence and absence of interactions between the charge and the pore. We find that the position of the charge that minimizes the translocation time in the absence of pore--polymer interactions is determined by the entropic cost of translocation, with the optimum charge position…
Motivated by a recent work on the metabolism of carbohydrates in bacteria, we study the kinetics and thermodynamics of two classic models for reversible polymerization, one preserving the total polymer concentration and the other one not. The chemical kinetics is described by rate equations following the mass-action law. We consider a closed system and nonequilibrium initial conditions and show that the system dynamically evolves towards equilibrium where detailed balance is satisfied. The entropy production during this process can be expressed as the time derivative of a Lyapunov function. Wh…
We investigate the nature of the effective dynamics and statistical forces obtained after integrating out nonequilibrium degrees of freedom. To be explicit, we consider the Rouse model for the conformational dynamics of an ideal polymer chain subject to steady driving. We compute the effective dynamics for one of the many monomers by integrating out the rest of the chain. The result is a generalized Langevin dynamics for which we give the memory and noise kernels and the effective force, and we discuss the inherited nonequilibrium aspects.
We study a model of two polymers confined to a slit with sticky walls. More precisely, we find and analyse the exact solution of two directed friendly walks in such a geometry on the square lattice. We compare the infinite slit limit, in which the length of the polymer (thermodynamic limit) is taken to infinity before the width of the slit is considered to become large, to the opposite situation where the order of the limits are swapped, known as the half-plane limit when one polymer is modelled. In contrast with the single polymer system we find that the half-plane and infinite slit limits co…
We study a generalized interacting self-avoiding walk (ISAW) model with nearest- and next nearest-neighbor (NN and NNN) interactions on the square and cubic lattices. In both dimensions, the phase diagrams show coil and globule phases separated by continuous transition lines. Along these lines, we calculate the metric $ν_t$, crossover $ϕ_t$ and entropic $γ_t$ exponents, all of them in good agreement with the exact values of the $Θ$ universality class. Therefore, the introduction of NNN interactions does not change the class of the ISAW model, which still exists even for repulsive forces. The g…
The adsorption of polydisperse ideal polymer chains is shown to be sensitive to the large N tail of the distribution of chains. If and only if the number of chains decays more slowly than exponentially then there is an adsorption transition like that of monodisperse infinite chains. If the number decays exponentially the adsorption density diverges continuously at a temperature which is a function of the mean chain length. At low coverages, chains with repulsive monomer--monomer interactions show the same qualitative behaviour
The impact of impenetrable obstacles on the energetics and equilibrium structure of strongly repulsive directed polymers is investigated. As a result of the strong interactions, regions of severe polymer depletion and excess are found in the vicinity of the obstacle, and the associated free-energy cost is found to scale quadratically with the average polymer density. The polymer-polymer interactions are accounted for via a sequence of transformations: from the 3D line liquid to a 2D fluid of Bose particles to a 2D composite fermion fluid and, finally, to a 2D one-component plasma. The results …
In this paper, we study the equilibrium properties of polymer chains end-tethered to a fluid membrane. The loss of conformational entropy of the polymer results in an inhomogeneous pressure field that we calculate for gaussian chains. We estimate the effects of excluded volume through a relation between pressure and concentration. Under the polymer pressure, a soft surface will deform. We calculate the deformation profile for a fluid membrane and show that close to the grafting point, this profile assumes a cone-like shape, independently of the boundary conditions. Interactions between differe…
We consider a lattice model of a mixture of repulsive, attractive, or neutral monodisperse star (species A) and linear (species B) polymers with a third monomeric species C, which may represent free volume. The mixture is next to a hard, infinite plate whose interactions with A and C can be attractive, repulsive, or neutral. These two interactions are the only parameters necessary to specify the effect of the surface on all three components. We numerically study monomer density profiles using the method of Gujrati and Chhajer that has already been previously applied to study polydisperse and m…
The exact grand-canonical solution of a generalized interacting self-avoid walk (ISAW) model, placed on a Husimi lattice built with squares, is presented. In this model, beyond the traditional interaction $ω_1=e^{ε_1/k_B T}$ between (nonconsecutive) monomers on nearest-neighbor (NN) sites, an additional energy $ε_2$ is associated to next-NN (NNN) monomers. Three definitions of NNN sites/interactions are considered, where each monomer can have, effectively, at most 2, 4 or 6 NNN monomers on the Husimi lattice. The phase diagrams found in all cases have (qualitatively) the same thermodynamic pro…
Driven diffusive systems constitute paradigmatic models of nonequilibrium physics. Among them, a driven lattice gas known as the asymmetric simple exclusion process (ASEP) is the most prominent example for which many intriguing exact results have been obtained. After summarizing key findings, including the mapping of the ASEP to quantum spin chains, we discuss the recently introduced Brownian asymmetric simple exclusion process (BASEP) as a related class of driven diffusive system with continuous space dynamics. In the BASEP, driven Brownian motion of hardcore-interacting particles through one…
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…
A {\it new} formula for the force vs extension relation is derived from the discrete version of the so called {\it worm like chain} model. This formula correctly fits some recent experimental data on polymer stretching and some numerical simulations with pairwise repulsive potentials. For a more realistic Lennard-Jones potential the agreement with simulations is found to be good when the temperature is above the $θ$ temperature. For lower temperatures a plateau emerges, as predicted by some recent experimental and theoretical results, and our formula gives good results only in the high force r…
In this work we survey selected theoretical developments for models of deposition of extended particles, with and without surface diffusion, on linear and planar substrates, of interest in colloid, polymer, and certain biological systems.
We report a numerical study of equilibrium phase-diagrams and interfacial properties of bulk and confined colloid-polymer mixtures using grand canonical Monte Carlo simulations. Colloidal particles are treated as hard spheres, while the polymer chains are described as soft repulsive spheres. The polymer-polymer, colloid-polymer, and wall-polymer interactions are described by density-dependent potentials derived by Bolhuis and Louis [Macromolecules, 35 (2002), p.1860]. We compared our results with those of the Asakura-Oosawa-Vrij model, that treats the polymers as ideal particles. We find that …
We investigate motility-induced phase separation of active Brownian particles, which are modeled as purely repulsive spheres that move due to a constant swim force with freely diffusing orientation. We develop on the basis of power functional concepts an analytical theory for nonequilibrium phase coexistence and interfacial structure. Theoretical predictions are validated against Brownian dynamics computer simulations. We show that the internal one-body force field has four nonequilibrium contributions: (i) isotropic drag and (ii) interfacial drag forces against the forward motion, (iii) a sup…
The glass transition, extensively studied in dense fluids, polymers, or colloids, corresponds to a dramatic evolution of equilibrium transport coefficients upon a modest change of control parameter, like temperature or pressure. A similar phenomenology is found in many systems evolving far from equilibrium, such as driven granular media, active and living matter. While many theories compete to describe the glass transition at thermal equilibrium, very little is understood far from equilibrium. Here, we solve the dynamics of a specific, yet representative, class of glass models in the presence …
We numerically examine the nonlinear rubber elasticity of topologically constrained polymer networks. We propose a simple and effective model based on Graessley and Pearson's topological model (GP model) for describing the topological effect. The main point is to take account of a nonequilibrium effect in the synthesis process of the polymer network. We introduce a new parameter $γ$ to describe entropic contributions from the entanglement of polymer loops, which may be determined from the structural characteristics of the sample. The model is evaluated in the light of experimental data under u…
We present results for the nonequilibrium dynamics of collapse for a model flexible homopolymer on simple cubic lattices with fixed and fluctuating bonds between the monomers. Results from our Monte Carlo simulations show that, phenomenologically, the sequence of events observed during the collapse are independent of the bond criterion. While the growth of the clusters (of monomers) at different temperatures exhibits a nonuniversal power-law behavior when the bonds are fixed, the introduction of fluctuations in the bonds by considering the existence of diagonal bonds produces a temperature ind…
We present a theory for the equilibrium structure of polyelectrolyte solutions. The main element is a simple, new optimization scheme that allows theories such as the random phase approximation (RPA) to handle the harsh repulsive forces present in such systems. Comparison is made with data from recent neutron scattering experiments of randomly charged, hydrophilic polymers in salt-free, semi-dilute solution at various charge densities. Models with varying degrees of realism are examined. The usual explanation of the invariance observed at high charge density has been counterion condensation. H…
By applying local primitive path and Rouse modes analysis we study the chains conformations, local dynamics and viscosity of a model polymer melt in a polymer-wall interface. We establish that the presence of a repulsive wall leads to acceleration of the dynamics both for unentangled and weakly entangled melts and to a depletion in the entanglement density in the wall vicinity. When the surface bears some grafted chains, we show that the melt chains are accelerated in the unentangled regime and slowed down in the entangled regime. By analyzing the primitive paths we attribute the observed slow…
The nonequilibrium free energy theorems show how distributions of work along nonequilibrium paths are related to free energy differences between the equilibrium states at the end points of these paths. In this paper we develop a natural way of barostatting a system and give the first deterministic derivation of the Crooks and Jarzynski relations for these isothermal isobaric systems. We illustrate these relations by applying them to molecular dynamics simulations of a model polymer undergoing stretching.
Solutions of interacting linear polymers are mapped onto a system of ``soft'' spherical particles interacting via an effective pair potential. This coarse-graining reduces the individual monomer-level description to a problem involving only the centers of mass (CM) of the polymer coils. The effective pair potentials are derived by inverting the CM pair distribution function, generated in Monte Carlo simulations, using the hypernetted chain (HNC) closure. The method, previously devised for the self-avoiding walk model of polymers in good solvent, is extended to the case of polymers in solvents …
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…
Paramagnetic colloidal particles that are optically trapped in a linear array can form a zigzag pattern when an external magnetic field induces repulsive interparticle interactions. When the traps are abruptly turned off, the particles form a nonequilibrium expanding pattern with a zigzag symmetry, even when the strength of the magnetic interaction is weaker than that required to break the linear symmetry of the equilibrium state. We show that the transition to the equilibrium zigzag state is always potentially possible for purely harmonic traps. For anharmonic traps that have a finite height,…
We study the induced interaction between multiple probes locally interacting with driven colloids and trapped in a toroidal geometry. The effective binary forces between the probes break the action-reaction principle and their range decreases with the driving. We demonstrate how in the stationary nonlinear nonequilibrium regime these interactions induce stability of a crystal-like pattern, where the probes are equidistant, when the probe-colloid interaction is either completely attractive or completely repulsive.
Dimensional reduction occurs when the critical behavior of one system can be related to that of another system in a lower dimension. We show that this occurs for directed branched polymers (DBP) by giving an exact relationship between DBP models in D+1 dimensions and repulsive gases at negative activity in D dimensions. This implies relations between exponents of the two models: $γ(D+1)=α(D)$ (the exponent describing the singularity of the pressure), and $ν_{\perp}(D+1)=ν(D)$ (the correlation length exponent of the repulsive gas). It also leads to the relation $θ(D+1)=1+σ(D)$, where $σ(D)$ is …
The number of configurations of a polymer is reduced in the presence of a barrier or an obstacle. The resulting loss of entropy adds a repulsive component to other forces generated by interaction potentials. When the obstructions are scale invariant shapes (such as cones, wedges, lines or planes) the only relevant length scales are the polymer size R_0 and characteristic separations, severely constraining the functional form of entropic forces. Specifically, we consider a polymer (single strand or star) attached to the tip of a cone, at a separation h from a surface (or another cone). At close…
The winding of a single polymer in thermal equilibrium around a repulsive cylindrical obstacle is perhaps the simplest example of statistical mechanics in a multiply connected geometry. As shown by S.F. Edwards, this problem is closely related to the quantum mechanics of a charged particle interacting with a Aharonov-Bohm flux. In another development, Pollock and Ceperley have shown that boson world lines in 2+1 dimensions with periodic boundary conditions, regarded as ring polymers on a torus, have a mean square winding number given by $<W^2> = 2n_s\hbar^2/mk_BT$, where $m$ is the boson mass …
A polymer repelled by unfavorable interactions with a uniform flat surface may still be pinned to attractive edges and corners. This is demonstrated by considering adsorption of a two-dimensional ideal polymer to an attractive corner of a repulsive wedge. The well-known mapping between the statistical mechanics of an ideal polymer and the quantum problem of a particle in a potential is then used to analyze the singular behavior of the unbinding transition of the polymer. The divergence of the localization length is found to be governed by an exponent that varies continuously with the angle (wh…
We study analytically and numerically the winding of directed polymers of length $t$ around each other or around a rod. Unconfined polymers in pure media have exponentially decaying winding angle distributions, the decay constant depending on whether the interaction is repulsive or neutral, but not on microscopic details. In the presence of a chiral asymmetry, the exponential tails become non universal. In all these cases the mean winding angle is proportional to $\ln t$. When the polymer is confined to a finite region around the winding center, e.g. due to an attractive interaction, the windi…
Lattice model of directed self avoiding walk is used to investigate adsorption properties of a semiflexible sequential copolymer chain on an impenetrable curved surface on a hexagonal lattice in two dimensions. Walks of the copolymer chains are directed in a direction away from the surface at a suitable value of monomer surface attraction, the copolymer chain gets adsorbed on the surface. To calculate exact value of monomer surface attraction, the directed walk model have been solved analytically using generating function method to discuss results when one type monomer of the copolymer chain h…
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…
As a rough model for the collective motions of cells and organisms we develop here the statistical mechanics of swarms of self-propelled particles. Our approach is closely related to the recently developed theory of active Brownian motion and the theory of canonical-dissipative systems. Free motion and motion of a swarms confined in an external field is studied. Briefly the case of particles confined on a ring and interacting by repulsive forces is studied. In more detail we investigate self-confinement by Morse-type attracting forces. We begin with pairs N = 2; the attractors and distribution…
