We investigate the properties of a system of semi-diluted polymers in the presence of charged groups and counter-ions, by means of self-consistent field theory. We study a system of polyelectrolyte chains grafted to a similarly, as well as an oppositely charged surface, solving a set of saddle-point equations that couple the modified diffusion equation for the polymer partition function to the Poisson-Boltzmann equation describing the charge distribution in the system. A numerical study of this set of equations is presented and comparison is made with previous studies. We then consider the case of semi-diluted, grafted polymer chains in the presence of charge-end-groups. We study the problem with self-consistent field as well as strong-stretching theory. We derive the corrections to the Milner-Witten-Cates (MWC) theory for weakly charged chains and show that the monomer-density deviates from the parabolic profile expected in the uncharged case. The corresponding corrections are shown to be dictated by an Abel-Volterra integral equation of the second kind. The validity of our theoretical findings is confirmed comparing the predictions with the results obtained within numerical self-consistent field theory.
We compute the distribution of the work done in stretching a Gaussian polymer, made of N monomers, at a finite rate. For a one-dimensional polymer undergoing Rouse dynamics, the work distribution is a Gaussian and we explicitly compute the mean and width. The two cases where the polymer is stretched, either by constraining its end or by constraining the force on it, are examined. We discuss connections to Jarzynski's equality and the fluctuation theorems.
Using molecular dynamic simulation, we study the stretching of an adsorbed homopolymer in a poor solvent with one end held at a distance $z_e$ from the substrate. We measure the vertical force $f$ on the end of the chain as a function of the extension $z_e$ and the substrate interaction energy $w$. The force reaches a plateau value at large extensions. In the strong adsorption limit, we show that the plateau value increase linearly in $w$ in good agreement with a theoretical model. In the weak adsorption limit, a polymer globule with a layered structure is formed and elastically deformed when …
We consider a linear polymer chain in a disordered environment modeled by percolation clusters on a square lattice. The disordered environment is meant to roughly represent molecular crowding as seen in cells. The model may be viewed as the simplest representation of biopolymers in a cell. We show the existence of intermediate states during stretching arising as a consequence of molecular crowding. In the constant distance ensemble the force-extension curves exhibit oscillations. We observe the emergence of two or more peaks in the probability distribution curves signaling the coexistence of d…
The way tension propagates along a chain is a key to govern many of anomalous dynamics in macromolecular systems. After introducing the weak and the strong force regimes of the tension propagation, we focus on the latter, in which the dynamical fluctuations of a segment in a long polymer during its stretching process is investigated. We show that the response, i.e., average drift, is anomalous, which is characterized by the nonlinear memory kernel, and its relation to the fluctuation is nontrivial. These features are discussed on the basis of the generalized Langevin equation, in which the rol…
The recently proposed fluctuation relation in unfolding forces [Phys. Rev. E ${\bf 84}$, $060101$(R) $(2011)$] is re-examined taking into account the explicit time dependence of the force distribution. The stretching of a tethered Rouse polymer is exactly solved and the ratio of the probabilities of positive to negative forces is shown to be an exponential in force. Extensive steered molecular dynamics simulations of unfolding of deca alanine peptide confirm the form of fluctuation relation proposed earlier, but with explicit correct time dependence of unfolding forces taken into account. From…
In this paper we present simulations of a surface-adsorbed polymer subject to an elongation force. The polymer is modelled by a self-avoiding walk on a regular lattice. It is confined to a half-space by an adsorbing surface with attractions for every vertex of the walk visiting the surface, and the last vertex is pulled perpendicular to the surface by a force. Using the recently proposed flatPERM algorithm, we calculate the phase diagram for a vast range of temperatures and forces. The strength of this algorithm is that it computes the complete density of states from one single simulation. We …
We study the peculiarities of stretching of globular polymer macromolecules in a disordered (crowded) environment, using the model of self-attracting self-avoiding walks on site-diluted percolative lattices in space dimensions d=3. Applying the pruned-enriched Rosenbluth chain-growth method (PERM), we construct the phase diagram of collapsed-extended state coexistence when varying temperature and stretching force. The change in shape characteristics of globular polymers under stretching is analyzed as well.
The unfolding of a polymer below the $θ$ point when pulled by an external force is studied both in d=2 on the lattice and in $d=3$ off lattice. A ground state analysis of finite length chains shows that the globule unfolds via multiple steps, corresponding to transitions between different minima, in both cases. In the infinite length limit, these intermediate minima have a qualitative effect only in $d=2$. The phase diagram in d=2 is determined using transfer matrix techniques. Energy-entropy and renormalization group arguments are given which predict a qualitatively correct phase diagram and …
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 …
We develop a strong stretching approximation for a polymer brush made of self-avoiding polymer chains. The density profile of the brush and the distribution of the end monomer positions in stretching direction are computed and compared with simulation data. We find that our approach leads to a clearly better approximation as compared to previous approaches based upon Gaussian elasticity at low grafting densities (moderate chain stretching), for which corrections due to finite extensibility can be ignored.
This article focuses on a preaveraging description of polymer nonequilibrium stretching, where a single polymer undergoes a transient process from equilibrium to nonequilibrium steady state by pulling one chain end. The preaveraging method combined with mode analysis reduces the original Langevin equation to a simplified form for both a stretched steady state and an equilibrium state, even in the presence of self-avoiding repulsive interactions spanning a long range. However, the transient stretching process exhibits evolution of a hierarchal regime structure, which means a qualitative tempora…
We analyze the statistics of work generated by a gradient flow to stretch a nonlinear polymer. We obtain the Large Deviation Function (LDF) of the work in the full range of appropriate parameters by combining analytical and numerical tools. The LDF shows two distinct asymptotes: "near tails" are linear in work and dominated by coiled polymer configurations, while "far tails" are quadratic in work and correspond to preferentially fully stretched polymers. We find the extreme value statistics of work for several singular elastic potentials, as well as the mean and the dispersion of work near the…
Extensional rheometry and Brownian Dynamics simulations of flexible polymer solutions confirm predictions based on blob concepts that coil--stretch hysteresis in extensional flows increases with concentration, reaching a maximum at the critical overlap concentration $c^\ast$ before progressively vanishing in the semidilute regime. These observations demonstrate that chain stretching strengthens intermolecular hydrodynamic screening in dilute solutions, but weakens it in semidilute solutions. Flow can thus strongly modify the concentration dependence of viscoelastic properties of polymer soluti…
We study the spontaneous out-of-plane bending of a planar untwisted ribbon composed of nematic polymer networks activated by a change in temperature. Our theory accounts for both stretching and bending energies, which compete to establish equilibrium. We show that when equilibrium is attained these energy components obey a \emph{complementarity} relation: one is maximum where the other is minimum. Moreover, we identify a \emph{bleaching} regime: for sufficiently large values of an activation parameter (which measures the mismatch between the degrees of order in polymer organization in the refe…
We investigate the stretching response of a thick polymer model by means of extensive stochastic simulations. The computational results are synthesized in an analytic expression that characterizes how the force versus elongation curve depends on the polymer structural parameters: its thickness and granularity (spacing of the monomers). The expression is used to analyze experimental data for the stretching of various different types of biopolymers: polypeptides, polysaccharides and nucleic acids. Besides recovering elastic parameters (such as the persistence length) that are consistent with tho…
We study flexible polymer macromolecules in a crowded (porous) environment, modelling them as self-attracting self-avoiding walks (SASAW) on site-diluted percolative lattices in space dimensions d=2, 3. The influence of stretching force on the polymer folding and properties of globule-coil transitions are analyzed. Applying the pruned-enriched Rosenbluth chain-growth method (PERM), we estimate the transition temperature T_Θ between collapsed and extended polymer configurations and construct the phase diagrams of the globule-coil coexistence when varying temperature and stretching force. The tr…
We consider an inextensible, semiflexible polymer or worm-like chain which is confined in the transverse direction by a parabolic potential and subject to a longitudinal force at the ends, so that the polymer is stretched out and backfolding is negligible. Simple analytic expressions for the partition function, valid in this regime, are obtained for chains of arbitrary length with a variety of boundary conditions at the ends. The spatial distribution of the end points or radial distribution function is also analyzed.
Behavior of a dilute polymer solution in a random three-dimensional flow with an average shear is studied experimentally. Polymer contribution to the shear stress is found to be more than two orders of magnitude higher than in a laminar shear flow. The results indicate that the polymer molecules get strongly stretched by the random motion of the fluid.
Using analytic theory, numerical calculation and Langevin dynamics simulation we demonstrate the existence of a first order unraveling transition in the stretching of a polymer chain in a poor solvent. The chain suddenly unravels from a "tadpole" or "ball and chain" configuration, to one where the ball shrinks to zero size. In the force curve this appears as a discontinuous drop in the force. This transition occurs under the conditions of most relevance for atomic force microscope experiments, where the extension is the independent variable. Our simulations show marked hysteresis as well as ma…
How hydrodynamic interactions alter polymer stretching in turbulence
IITB-Monash Research Academy, Indian Institute of Technology Bombay（印度孟买理工学院-蒙纳士大学联合研究院）；Indian Institute of Technology Bombay（印度孟买理工学院）；Monash University（蒙纳士大学）；Université Côte d’Azur（蔚蓝海岸大学）
It has long been known for elastomers that the velocity of crack propagation jumps as a function of strain. On the other hand, such a jump has not been reported in the literature for polymers which do not exhibit a rubbery plateau in the storage-modulus plot. Here, we report observation of jumps in crack propagation for semi-crystalline polymer sheets without the rubbery plateau, as a result of pulling the sheets at a constant speed. We discuss the advantages of this crack-propagation test under constant-speed stretching and provide physical interpretation of the velocity jump observed for non…
Polybutene-1 (PB-1), a typical semicrystalline polymer, in its stable form I shows a peculiar temperature dependent strain-whitening behavior when being stretched at different temperatures where the extent of strain-whitening weakens with the increasing of stretching temperature reaching a minima value followed by an increase at higher stretching temperatures. Correspondingly, a stronger strain-hardening phenomenon was observed at higher stretching temperatures. The strain-whitening phenomenon in semicrystalline polymers has its origin of cavitation process during stretching. In this work, the…
Polymers in a turbulent flow are stretched out by the fluctuating velocity gradient; the stationary probability distribution function (p.d.f.) of extensions $R$ has a power-law tail with an exponent that increases with the Weissenberg number $Wi$, a nondimensional measure of polymer elasticity. This study addresses the following questions: (i) What is the role of the non-Gaussian statistics of the turbulent velocity gradient on polymer stretching? (ii) How does the p.d.f. of $R$ evolve to its asymptotic stationary form? Our analysis is based on simulations of the dynamics of finitely-extensibl…
We present Monte Carlo data for a linear chain with excluded volume subjected to a uniform stretching. Simulation of long chains (up to 6000 beads) at high stretching allows us to observe the signature of tensile blobs as a crossover in the scaling behavior of the chain scattering function for wave vectors perpendicular to stretching. These results and corresponding ones in the stretching direction allow us to verify for the first time Pincus prediction on scaling inside blobs. Outside blobs, the scattering function is well described by the Debye function for a stretched ideal chain.
While stretching of a polymer along a flat surface is hardly different from the classical Pincus problem of pulling chain ends in free space, the role of curved geometry in conformational statistics of the stretched chain is an exciting open question. Here by means of the scaling analyses and computer simulations we examine stretching of a fractal polymer chain around a disc in 2D (or a cylinder in 3D) of radius $R$. Surprisingly, we reveal that the typical excursions of the polymer away from the surface scale as $Δ\sim R^β$, with the Kardar-Parisi-Zhang (KPZ) growth exponent $β=1/3$, for any …
Langevin Dynamics simulations of polymer translocation are performed where the polymer is stretched via two opposing forces applied on the first and last monomer before and during translocation. In this setup, polymer translocation is achieved by imposing a bias between the two pulling forces such that there is net displacement towards the \textit{trans}-side. Under the influence of pre-stretching forces, the elongated polymer ensemble contains less variations in conformations compared to an unstretched ensemble. Simulations demonstrate that this reduced spread in initial conformations yields …
We elucidate the elastic behavior of a wormlike chain in 3D under compression and provide exact solutions for the experimentally accessible force-extension relation in terms of generalized spheroidal wave functions. In striking contrast to the classical Euler buckling instability, the force-extension relation of a clamped semiflexible polymer exhibits a smooth crossover from an almost stretched to a buckled configuration. In particular, the associated susceptibility, which measures the strength of the response of the polymer to the applied force, displays a prominent peak in the vicinity of th…
We present a tube model for the Brownian dynamics of associating polymers in extensional flow. In linear response, the model confirms the analytical predictions for the sticky diffusivity by Leibler- Rubinstein-Colby theory. Although a single-mode DEMG approximation accurately describes the transient stretching of the polymers above a 'sticky' Weissenberg number (product of the strain rate with the sticky-Rouse time), the pre-averaged model fails to capture a remarkable development of a power-law distribution of stretch in steady-state extensional flow: while the mean stretch is finite, the fl…
We show that the problem of describing the conformations of a semiflexible polymer confined to a channel can be mapped onto an exactly solvable model in the so-called extended de Gennes regime. This regime (where the polymer is neither weakly nor strongly confined) has recently been studied intensively experimentally and by means of computer simulations. The exact solution predicts precisely how the conformational fluctuations depend upon the channel width and upon the microscopic parameters characterising the physical properties of the polymer.
Recent developments of microscopic mechanical experiments allow the manipulation of individual polymer molecules in two main ways: \textit{uniform} stretching by external forces and \textit{non-uniform} stretching by external fields. Many results can be thereby obtained for specific kinds of polymers and specific geometries. In this work we describe the non-uniform stretching of a single, non-branched polymer molecule by an external field (e.g. fluid in uniform motion, or uniform electric field) by a universal physical framework which leads to general conclusions on different types of polymers…
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 develop further a statistical model coupling denaturation and chain conformations in DNA (Palmeri J, Manghi M and Destainville N 2007 Phys. Rev. Lett. 99 088103). Our Discrete Helical Wormlike Chain model takes explicitly into account the three elastic degrees of freedom, namely stretching, bending and torsion of the polymer. By integrating out these external variables, the conformational entropy contributes to bubble nucleation (opening of base-pairs), which sheds light on the DNA melting mechanism. Because the values of monomer length, bending and torsional moduli differ significantly in …
We study the mechanical properties of semiflexible polymers when the contour length of the polymer is comparable to its persistence length. We compute the exact average end-to-end distance and shape of the polymer for different boundary conditions, and show that boundary effects can lead to significant deviations from the well-known long-polymer results. We also consider the case of stretching a uniformly charged biopolymer by an electric field, for which we compute the average extension and the average shape, which is shown to be trumpetlike. Our results also apply to long biopolymers when th…
We analyze static properties of a strongly confined semiflexible polymer, i.e. either trapped in a closed space or compressed by external forces, in an athermal solvent. Like a flexible polymer case, we can resort to an analogy with the semidilute solution, but a complication due to the additional length scale arising from the chain rigidity results in more diverse behaviours depending on system parameters. For each regime, scaling forms of the excess free energy of the confinement are derived. Effects of the confinement geometry and the solvent quality are briefly discussed.
We study the conformational properties of polymers in presence of extended columnar defects of parallel orientation. Two classes of macromolecules are considered: the so-called partially directed polymers with preferred orientation along direction of the external stretching field and semiflexible polymers. We are working within the frames of lattice models: partially directed self-avoiding walks (PDSAWs) and biased self-avoiding walks (BSAWs). Our numerical analysis of PDSAWs reveals, that competition between the stretching field and anisotropy caused by presence of extended defects leads to e…
The dynamic behavior of semi-dilute polymer solutions is governed by an interplay between solvent quality, concentration, molecular weight, and flow type. Semi-dilute solutions are characterized by large fluctuations in concentration, wherein polymer coils interpenetrate but may not be topologically entangled at equilibrium. In non-equilibrium flows, it is generally thought that polymer chains can self-entangle in semi-dilute solutions, thereby leading to entanglements in solutions that are nominally unentangled at equilibrium. Despite recent progress, we still lack a complete molecular-level …
The sliding of non-Newtonian drops down planar surfaces results in a complex, entangled balance between interfacial forces and non linear viscous dissipation, which has been scarcely inspected. In particular, a detailed understanding of the role played by the polymer flexibility and the resulting elasticity of the polymer solution is still lacking. To this aim, we have considered polyacrylamide (PAA) solutions of different molecular weights, suspended either in water or glycerol/water mixtures. In contrast to drops with stiff polymers, drops with flexible polymers exhibit a remarkable elongati…
We analyze the nonequilibrium dynamics of single inextensible semiflexible biopolymers as stretching forces are applied at the ends. Based on different (contradicting) heuristic arguments, various scaling laws have been proposed for the propagation speed of the backbone tension which is induced in response to stretching. Here, we employ a newly developed unified theory to systematically substantiate, restrict, and extend these approaches. Introducing the practically relevant scenario of a chain equilibrated under some prestretching force $f_\text{pre}$ that is suddenly exposed to a different e…
We present a theory for the elasticity of cross-linked stiff polymer networks. Stiff polymers, unlike their flexible counterparts, are highly anisotropic elastic objects. Similar to mechanical beams stiff polymers easily deform in bending, while they are much stiffer with respect to tensile forces (``stretching''). Unlike in previous approaches, where network elasticity is derived from the stretching mode, our theory properly accounts for the soft bending response. A self-consistent effective medium approach is used to calculate the macroscopic elastic moduli starting from a microscopic charac…
We investigate the pseudo-Casimir force in a slab of material composed of nematically ordered long polymers. We write the total mesoscopic energy together with the constraint connecting the local density and director fluctuations and evaluate the corresponding fluctuation free energy by standard methods. It leads to a pseudo-Casimir force of a different type than in the case of standard, short molecule nematic. We investigate its separation dependence and its magnitude and explicitly derive the relevant limiting cases.
Nematic polymeric networks are (heat and light) activable materials, which combine the features of rubber and nematic liquid crystals. When only the stretching energy of a thin sheet of nematic polymeric network is minimized, the intrinsic (Guassian) curvature of the shape it takes upon (thermal or optical) actuation is determined. This, unfortunately, produces a multitude of possible shapes, for which we need a selection criterion, which may only be provided by a correcting bending energy depending on the extrinsic curvatures of the deformed shape. The literature has so far offered approximat…
The quite recent technological rise in molecular biology allowed single molecule manipulation experiments, where molecule stretching plays a primary role. In order to understand the experimental data, it is felt the urge of some physical and mathematical models to quantitatively express the mechanical properties of the observed molecules. In this paper we reconsider a simple phenomenological model which reproduces the behaviour of single and double stranded DNA under tension. The problem is easily solved via the cavity method both in the small forces range and in presence of overstretching tra…
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.
Theories of strongly stretched polymer brushes, particularly the parabolic brush theory, are valuable for providing analytically tractable predictions for the thermodynamic behavior of surface-grafted polymers in a wide range of settings. However, the parabolic brush limit fails to describe polymers grafted to convex, curved substrates, such as the surfaces of spherical nanoparticles or the interfaces of strongly segregated block copolymers. It has been previously shown that strongly-stretched, curved brushes require a boundary layer devoid of free chain ends, requiring modifications of the th…
The dynamics of elastocapillary thinning in high molecular weight polymer solutions are re-examined using high-speed digital video microscopy. At long times, the evolution of the viscoelastic thread deviates from self-similar exponential decay and competition of elastic, capillary and inertial forces leads to the formation of a periodic array of beads connected by axially-uniform ligaments. This configuration is itself unstable and successive instabilities propagate from the necks connecting the beads and ligaments. This iterated process results in the development of multiple generations of be…
We consider the dynamics of polymer translocation out of confined environments. Analytic scaling arguments lead to the prediction that the translocation time scales like $τ\sim N^{β+ν_{2D}}R^{1+(1-ν_{2D})/ν}$ for translocation out of a planar confinement between two walls with separation $R$ into a 3D environment, and $τ\sim N^{β+1}R$ for translocation out of two strips with separation $R$ into a 2D environment. Here, $N$ is the chain length, $ν$ and $ν_{2D}$ are the Flory exponents in 3D and 2D, and $β$ is the scaling exponent of translocation velocity with $N$, whose value for the present ch…
We study the relaxation dynamics of a coarse-grained polymer chain at different degrees of stretching by both analytical means and numerical simulations. The macromolecule is modelled as a string of beads, connected by anharmonic springs, subject to a tensile force applied at the end monomer of the chain while the other end is fixed at the origin of coordinates. The impact of bond non-linearity on the relaxation dynamics of the polymer at different degrees of stretching is treated analytically within the Gaussian self-consistent approach (GSC) and then compared to simulation results derived fr…
Stretching dynamics of polymers in microfluidics is of particular interest for polymer scientists. As a charged polymer, a polyelectrolyte can be deformed from its coiled equilibrium configuration to an extended chain by applying uniform or non-uniform electric fields. By means of hybrid lattice Boltzmann-molecular dynamics simulations, we investigate how the condensed counterions around the polyelectrolyte contribute to the polymer stretching in inhomogeneous fields. As an application, we discuss the translocation phenomena and entropic traps, when the driving force is an applied external ele…
The stretching of brushes of long polymers grafted to a planar surface is investigated byMonte Carlo simulations in the limit of very high grafting densities, as achieved in recent experiments. The monomer density profiles are shown to deviate considerably from the parabolic limiting form predicted by self-consistent field theory. A rapid transition is observed from parabolic to fully stretched polymers, characterized by a dramatic change in the end-monomer height distribution and by a clear cross-over in the slope of the brush height versus scaled grafting density.
We study long polymer chains in a poor solvent, confined to the space between two parallel hard walls. The walls are energetically neutral and pose only a geometric constraint which changes the properties of the coil-globule (or "$θ$-") transition. We find that the $θ$ temperature increases monotonically with the width $D$ between the walls, in contrast to recent claims in the literature. Put in a wider context, the problem can be seen as a dimensional cross over in a tricritical point of a $ϕ^4$ model. We roughly verify the main scaling properties expected for such a phenomenon, but we find a…
Semiflexible macromolecules in dilute solution under very good solvent conditions are modeled by self-avoiding walks on the simple cubic lattice ($d=3$ dimensions) and square lattice ($d=2$ dimensions), varying chain stiffness by an energy penalty $ε_b$ for chain bending. In the absence of excluded volume interactions, the persistence length $\ell_p$ of the polymers would then simply be $\ell_p=\ell_b(2d-2)^{-1}q_b^{-1}$ with $q_b= \exp(-ε_b/k_BT)$, the bond length $\ell_b$ being the lattice spacing, and $k_BT$ is the thermal energy. Using Monte Carlo simulations applying the pruned-enriched R…
