We present exact and analytically accurate results for the problem of a flexible polymer chain in shear flow. Under such a flow the polymer tumbles, and the probability distribution of the tumbling times $τ$ of the polymer decays exponentially as $\sim \exp(-ατ/τ_0)$ (where $τ_0$ is the longest relaxation time). We show that for a Rouse chain, this nontrivial constant $α$ can be calculated in the limit of large Weissenberg number (high shear rate) and is in excellent agreement with our simulation result of $α\simeq 0.324$. We also derive exactly the distribution functions for the length and the orientational angles of the end-to-end vector of the polymer.
We investigate the molecular origin of shear-thinning in melts of flexible, semiflexible and rigid oligomers with coarse-grained simulations of a sheared melt. Alignment, stretching and tumbling modes or suppression of the latter all contribute to understanding how macroscopic flow properties emerge from the molecular level. By performing simulations of single chains in a shear flow, we identify which of these phenomena are of collective nature and arise through interchain interactions and which are already present in dilute systems. Building upon these microscopic simulations we identify by m…
The non-equilibrium structural and dynamical properties of semiflexible polymers confined to two dimensions are investigated by molecular dynamics simulations. Three different scenarios are considered: The force-extension relation of tethered polymers, the relaxation of an initially stretched semiflexible polymer, and semiflexible polymers under shear flow. We find quantitative agreement with theoretical predictions for the force-extension relation and the time dependence of the entropically contracting polymer. The semiflexible polymers under shear flow exhibit significant conformational chan…
We have developed a dynamic self-consistent field theory, without any adjustable parameters, for unentangled polymer blends under shear. Our model accounts for the interaction between polymers, and enables one to compute the evolution of the local rheology, microstructure and the conformations of the polymer chains under shear self-consistently. We use this model to study the interfacial dynamics in sheared polymer blends and make a quantitative comparison between this model and Molecular Dynamics simulations. We find good agreement between the two methods.
We investigate nonlinear rheology of dilute liquid crystalline polymer solutions under time dependent two-directional shear flow. We analyze the Smoluchowski equation, which describes the dynamics of the orientation of a liquid crystalline polymer, by employing technique of the full counting statistics. In the adiabatic limit, we derive the expression for time integrated currents generated by a Berry-like curvature. Using this expression, it is shown that the expectation values of the time-integrated angular velocity of a liquid crystalline polymer and the time-integrated stress tensor are gen…
We investigate the viscoelastic properties of entangled networks of semiflexible polymers. At intermediate time scales the elastic response of these networks to shear deformation is described by the plateau modulus $G$. Different scaling laws with polymer concentration $c$ have been proposed based on the assumption that the deformation field is affine on all length scales. We develop a numerical approach that allows to calculate the modulus via free energy changes for both affine and non-affine deformations. The non-affine deformation field is obtained by a free energy minimization. Our findin…
We study analytically a model of a two dimensional, partially directed, flexible or semiflexible polymer, attached to an attractive wall which is perpendicular to the preferred direction. In addition, the polymer is stretched by an externally applied force. We find that the wall has a dramatic effect on the polymer. For wall attraction smaller than the non-sequential nearest neighbor attraction, the fraction of monomers at the wall is zero and the model is the same as that of a polymer without a wall. However, for greater than, the fraction of monomers at the wall undergoes a first order trans…
We have mapped the physics of a system of semi-flexible inextensible polymers onto a complex Ginzburg-Landau field theory using techniques of functional integration. It is shown in the limit of low number density of monomers in a melt of semi-flexible, inextensible polymers, kept apart by an excluded volume interaction, the radius of gyration scales as N^{nu}, where N is the chain length, and nu = 1, in contrast to the value of nu ~ 0.6 for flexible polymer melts. Using Renormalization Group arguments, we show that the system exhibits an infra-red stable fixed point which can be identified as …
We consider random walk model of a semi-flexible polymer chain on a square and a cubic lattice to enumerate conformations of the polymer chain in two and three dimensions, respectively. The bending energy of the chain is assumed as the key factor which controls the minimum average length of the chain in between two successive bends in the chain; and the average length of the chains per unit bend is defined as the persistence length of the polymer chain. It has been found that the minimum energy required to bend the chain is expressed in the form of simple relation which includes space dimensio…
Recent experiments suggest that shear-enhanced growth of concentration fluctuations in polymer solutions is strongly influenced by solid boundaries. We analyze the dynamics of a model of a sheared polymer solution, accounting for the effect of stress variations on mass flux and for wall-slip. If (and only if) these effects are present, the flow exhibits a boundary-localized instability consistent with experimental observations. Even in the absence of flow instability, thermally-driven concentration fluctuations are significantly enhanced near the boundary.
The effect of excluded volume interactions on the structure of a polymer in shear flow is investigated by Brownian Dynamics simulations for chains with size $30\leq N\leq 300$. The main results concern the structure factor $S({\bf q})$ of chains of N=300 Kuhn segments, observed at a reduced shear rate $β=\dotγτ=3.2$, where $\dotγ$ is the bare shear rate and $τ$ is the longest relaxation time of the chain. At low q, where anisotropic global deformation is probed, the chain form factor is shown to match the form factor of the continuous Rouse model under shear at the same reduced shear rate, com…
Using molecular simulations, we study the properties of a polymer brush in contact with an explicit solvent under Couette and Poiseuille flow. The solvent is comprised of chemically identical chains. We present evidence that individual, unentangled chains in the dense brush exhibit cyclic, tumbling motion and non-Gaussian fluctuations of the molecular orientations similar to the behaviour of isolated tethered chains in shear flow. The collective molecular motion gives rise to an inversion of hydrodynamic flow direction in the vicinity of the brush-coated surface. Utilising Couette and Poiseuil…
We numerically investigate viscoelastic phase separation in polymer solutions under shear using a time-dependent Ginzburg-Landau model. The gross variables in our model are the polymer volume fraction and a conformation tensor. The latter represents chain deformations and relaxes slowly on the rheological time giving rise to a large viscoelastic stress. The polymer and the solvent obey two-fluid dynamics in which the viscoelastic stress acts asymmetrically on the polymer and, as a result, the stress and the diffusion are dynamically coupled. Below the coexistence curve, interfaces appear with …
The growing importance of microfluidic and nanofluidic devices to the study of biological processes has highlighted the need to better understand how confinement affects the behavior of polymers in flow. In this paper we explore one aspect of this question by calculating the steady-state extension of a long polymer chain in a narrow capillary tube in the presence of simple shear. The calculation is carried out within the framework of the Rouse-Zimm approach to chain dynamics, using a variant of a nonlinear elastic model to enforce finite extensibility. Under the assumption that the sole effect…
The role of solvent quality in determining the universal material properties of dilute polymer solutions undergoing steady simple shear flow is examined. A bead-spring chain representation of the polymer molecule is used, and the influence of solvent molecules on polymer conformations is modelled by a narrow Gaussian excluded volume potential that acts pair-wise between the beads of the chain. Brownian dynamics simulations data, acquired for chains of finite length, and extrapolated to the limit of infinite chain length, are shown to be model independent. This feature of the narrow Gaussian po…
Molecular dynamics simulations are performed for a polymer melt composed of short chains in quiescent and sheared conditions. The stress relaxation function $G(t)$ exhibits a stretched exponential form in a relatively early stage and ultimately follows the Rouse function in quiescent supercooled state. Transient stress evolution after application of shear obeys the linear growth $\int_0^t dt'G(t')$ for strain less than 0.1 and then saturates into a non-Newtonian viscosity. In steady states, strong shear-thinning and elongation of chains into ellipsoidal shapes are found at extremely small shea…
We consider the escape of a flexible, self-avoiding polymer chain out of a confined geometry. By means of simulations, we demonstrate that the translocation time can be described by a simple scaling law that exhibits a nonlinear dependence on the degree of polymerization and that is sensitive to the nature of the confining geometry. These results contradict earlier predictions but are in agreement with recently confirmed geometry-dependent expressions for the free energy of confinement.
We investigate by means of molecular dynamics simulation a coarse-grained polymer glass model focusing on (quasi-static and dynamical) shear-stress fluctuations as a function of temperature T and sampling time $Δt$. The linear response is characterized using (ensemble-averaged) expectation values of the contributions (time-averaged for each shear plane) to the stress-fluctuation relation $μ_{sf}$ for the shear modulus and the shear-stress relaxation modulus $G(t)$. Using 100 independent configurations we pay attention to the respective standard deviations. While the ensemble-averaged modulus $…
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…
We investigate the binding transition of two flexible polymers grafted to a steric surface with closeby end points. While free polymers show a discontinuous transition, grafting to a steric flat surface leads to a continuous binding transition. This is supported by results from Metropolis and parallel multicanonical simulations. A combination of canonical and microcanonical analyses reveals that the change in transition order can be understood in terms of the reduced translational entropy of the unbound high-temperature phase upon grafting.
Polymers in shear flow are ubiquitous and we study their motion in a viscoelastic fluid under shear. Employing dumbbells as representative, we find that the center of mass motion follows: $\langle x^2_c(t) \rangle \sim \dotγ^2 t^{α+2}, ~0< α<1$, generalizing the earlier result: $\langle x^2_c(t) \rangle \sim \dotγ^2t^3 ~(α= 1)$. Motion of the relative coordinate, on the other hand, is quite intriguing in that $\langle x^2_r(t) \rangle \sim t^β$ with $β= 2(1-α)$ for small $α$. This implies nonexistence of the steady state. We remedy this pathology by introducing a nonlinear spring with FENE-LJ …
We study the behavior of a flexible polymer chain in the presence of a low-molecular weight solvent in the vicinity of a liquid-gas critical point within the framework of a self-consistent field theory. The total free energy of the dilute polymer solution is expressed as a function of the radius of gyration of the polymer and the average solvent number density within the gyration volume at the level of the mean-field approximation. Varying the strength of attraction between polymer and solvent we show that two qualitatively different regimes occur at the liquid-gas critical point. In case of w…
We report Monte Carlo simulations of the self-assembly of supramolecular polymers based on a model of patchy particles. We find a first-order phase transition, characterized by hysteresis and nucleation, toward a solid bundle of polymers, of length much greater than the average gas phase length. We argue that the bundling transition is the supramolecular equivalent of the sublimation transition, that results from a weak chain-chain interaction. We provide a qualitative equation of state that gives physical insight beyond the specific values of the parameters used in our simulations.
Considering the dynamics of a polymer with finite extensibility placed in a chaotic flow with large mean shear, we explain how the statistics of polymer extension changes with Weissenberg number, ${\it Wi}$, defined as the product of the polymer relaxation time and the Lyapunov exponent of the flow. Four regimes, of the ${\it Wi}$ number, are identified. One below the coil-stretched transition and three above the coil-stretched transition. Specific emphasis is given to explaining these regimes in terms of the polymer dynamics.
Using a lattice-based Monte Carlo code for simulating self-avoiding flexible polymers in three dimensions in the absence of explicit hydrodynamics, we study their Rouse modes. For self-avoiding polymers, the Rouse modes are not expected to be statistically independent; nevertheless, we demonstrate that numerically these modes maintain a high degree of statistical independence. Based on high-precision simulation data we put forward an approximate analytical expression for the mode amplitude correlation functions for long polymers. From this, we derive analytically and confirm numerically severa…
We study the statistical mechanics of double-stranded semi-flexible polymers using both analytical techniques and simulation. We find a transition at some finite temperature, from a type of short range order to a fundamentally different sort of short range order. In the high temperature regime, the 2-point correlation functions of the object are identical to worm-like chains, while in the low temperature regime they are different due to a twist structure. In the low temperature phase, the polymers develop a kink-rod structure which could clarify some recent puzzling experiments on actin.
The contact of a hydrogel during the rotational shearing on glass surface in concentrated polymer solution was observed in situ. Dynamic contact patterns that rotate in-phase with the rotational shearing of the gel were observed for the first time. The contact patterns with a periodicity in the circumferential direction appeared and developed into fine characters with the shearing time. The patterns appeared more quickly at elevated sliding velocity, polymer concentration, and normal pressure. Furthermore, the softness of the gel also substantially influenced the character of the patterns. The…
A polymer placed in chaotic flow with large mean shear tumbles, making a-periodic flips. We describe the statistics of angular orientation, as well as of tumbling time (separating two subsequent flips) of polymers in this flow. The probability distribution function (PDF) of the polymer orientation is peaked around a shear-preferred direction. The tails of this angular PDF are algebraic. The PDF of the tumbling time, $τ$, has a maximum at the value estimated as inverse Lyapunov exponent of the flow. This PDF shows an exponential tail for large $τ$ and a small-$τ$ tail determined by the simultan…
The quasi--equilibrium or maximum entropy approximation is applied in order to derive constitutive equations from kinetic models of polymer dynamics. It is shown in general and illustrated for an example how canonical distribution functions are obtained from the maximum entropy principle, how macroscopic and constitutive equations are derived therefrom and how these constitutive equations can be implemented numerically. In addition, a measure for the accuracy of the quasi--equilibrium approximation is proposed that can be evaluated while integrating the constitutive equations. In the example c…
We study the model of a partially directed flexible or semi-flexible homopolymer on a square lattice, subject to an externally applied force, in a direction either parallel to, or perpendicular to the preferred direction. The polymer is self-interacting and can therefore undergo a collapse transition. We show that this model can be solved and we obtain the force-temperature phase diagrams which, for the case of flexible polymers, agree with that of Brak et al obtained using a different method. At sufficiently low temperatures, the polymer conformation changes from compact to coil state as the …
Using molecular dynamics simulation of a polymer glass model we investigate free-standing polymer films focusing on the in-plane shear modulus $μ$ and the corresponding shear-stress relaxation modulus $G(t)$ as functions of temperature $T$, film thickness $H$ (tuned by means of the lateral box size $L$) and sampling time $Δt$. Various observables are seen to vary linearly with $1/H$ demonstrating thus the (to leading order) linear superposition of bulk and surface properties. In agreement with recent studies on three-dimensional polymer glass-formers, $μ$ and $G(t)$ are found to decrease conti…
We investigate the static shear viscosity on the sol side of the vulcanization transition within a minimal mesoscopic model for the Rouse-dynamics of a randomly crosslinked melt of phantom polymers. We derive an exact relation between the viscosity and the resistances measured in a corresponding random resistor network. This enables us to calculate the viscosity exactly for an ensemble of crosslinks without correlations. The viscosity diverges logarithmically as the critical point is approached. For a more realistic ensemble of crosslinks amenable to the scaling description of percolation, we …
We employ the recently introduced generalized microcanonical inflection point method for the statistical analysis of phase transitions in flexible and semiflexible polymers and study the impact of the bending stiffness upon the character and order of transitions between random-coil, globules, and pseudocrystalline conformations. The high-accuracy estimates of the microcanonical entropy and its derivatives required for this study were obtained by extensive replica-exchange Monte Carlo simulations. We observe that the transition behavior into the compact phases changes qualitatively with increas…
We consider a single Rouse polymer chain in two dimensions in presence of a transverse shear flow along the $x$ direction and calculate the persistence probability $P_0(t)$ that the $x$ coordinate of a bead in the bulk of the chain does not return to its initial position up to time $t$. We show that the persistence decays at late times as a power law, $P_0(t)\sim t^{-θ}$ with a nontrivial exponent $θ$. The analytical estimate of $θ=0.359...$ obtained using an independent interval approximation is in excellent agreement with the numerical value $θ\approx 0.360\pm 0.001$.
We present a theoretical description of the dynamics of a semi-flexible polymer being pulled through a nanopore by an external force acting at the pore. Our theory is based on the tensile blob picture of Pincus in which the front of the tensile force propagates through the backbone of the polymer, as suggested by Sakaue and recently applied to study a completely flexible polymer with self-avoidance, by Dubbledam et al. For a semi-flexible polymer with a persistence length P , its statistics is self-avoiding for a very long chain. As the local force increases, the blob size starts to decrease. …
Many theoretical works have attempted to coarse grain gene expression at the level of transcription and translation via frameworks based on exclusion processes. Usually in these models the three-dimensional conformation of the substrates (DNA and mRNA) is neglected, and particles move on a static unidimensional lattice in contact to an infinite reservoir. In this work we generalise the paradigmatic exclusion process and study the transport of particles along a unidimensional polymer-like flexible lattice immersed in a three-dimensional particle reservoir. We study the recycling of particles in…
We study the stochastic resonance (SR) of a flexible polymer chain crossing over a piecewise linear bistable potential. The dependence of signal to noise ratio $SNR$ on noise intensity $D$, coupling constant $k$ and polymer length $N$ is studied via two state approximation. We find that the response of signal to the background noise strength is significant at optimum values of $D_{opt}$, $k_{opt}$ and $N_{opt}$ which suggests novel means of manipulating proteins or vesicles. Furthermore, the thermally activated barrier crossing rate $r_{k}$ for the flexible polymer chain is studied. We find th…
A phase diagram for a surface-interacting long flexible polymer chain in a two-dimensional poor solvent where the possibility of collapse exists is determined using exact enumeration method. A model of a self-attracting self avoiding walk (SASAW) on a square lattice was considered and up to 28 steps in series were evaluated. A new adsorbed state having the conformation of a surface attached globule is found. Four phases (i) desorbed expanded, (ii) desorbed collapsed, (iii) adsorbed expanded and (iv) surface attached globule are found to meet at a point on the adsorption line.
We analyze the structural behavior of a single polymer chain grafted to an attractive, flexible surface. Our model is composed of a coarse-grained bead-and-spring polymer and a tethered membrane. By means of extensive parallel tempering Monte Carlo simulations it is shown that the system exhibits a rich phase behavior ranging from highly ordered, compact to extended random coil structures and from desorbed to completely adsorbed or even partially embedded conformations. These findings are summarized in a pseudophase diagram indicating the predominant class of conformations as a function of the…
Configurations of a single semiflexible polymer is studied when it is pushed into a nanochannel in the case where the polymer persistence length $l_p$ is much longer than the channel diameter $D$, i.e. $l_p/D \gg 1$. Using numerical simulations, we show that the polymer undergoes a sequence of recurring structural transitions upon longitudinal compression, i.e. random deflection along the channel, helix going around the channel wall, double-fold random deflection, double-fold helix, etc. We find that the helix transition can be understood as buckling of deflection segments, and the initial hel…
We consider the van der Waals interaction between a pair of polymers with quenched heterogeneous sequences of local polarizabilities along their backbones, and study the effective pairwise interaction energy for both stiff polymers and flexible Gaussian coils. In particular, we focus on the cases where the pair of polarizability sequences are (i)~distinct and (ii)~identical. We find that the pairwise interaction energies of distinct and identical Gaussian coils are both isotropic and exhibit the same decay behavior for separations larger than the gyration radius, in contradistinction to the or…
