Conformational fluctuations of a tethered polymer in uniform flow

The decay of correlations in the conformational fluctuations of a tethered polymer subjected to a uniform flow is analyzed in terms of relaxation times and associated normal modes. These quantities are calculated numerically from Brownian dynamics simulations of several bead spring polymer models. In this way, the influence of different effects like a finite extensibility of the springs and excluded-volume as well as hydrodynamic interactions between the beads on the decay of fluctuations is identified. Moreover, by comparison of the simulation results to analytically tractable blob models with corresponding assumptions, the capability of the tensile-blob picture to predict relaxation times and modes is assessed. For excluded-volume and hydrodynamic interactions a crossover to Rouse-like behavior occurs when the flow velocity and hence the polymer deformation exceeds a certain value. For finitely extensible springs, in contrast, the relaxation times decrease monotonically with increasing polymer deformation. This latter behavior differs from assumptions often used in rheological modeling by dumbbells and is not captured by the blob model.Received: 4 April 2003, Published online: 12 August 2003PACS: 83.80.Rs Polymer solutions - 83.10.Mj Molecular dynamics, Brownian dynamics - 36.20.Ey Conformation (statistics and dynamics) - 47.50. + d Non-Newtonian fluid flows     

The electrostatic persistence length of polymers beyond the OSF limit

We use large-scale Monte Carlo simulations to test scaling theories for the electrostatic persistence length l _e of isolated, uniformly charged polymers with Debye-Hückel intrachain interactions in the limit where the screening length κ^-1 exceeds the intrinsic persistence length of the chains. Our simulations cover a significantly larger part of the parameter space than previous studies. We observe no significant deviations from the prediction l _e∝κ^-2 by Khokhlov and Khachaturian which is based on applying the Odijk-Skolnick-Fixman theories of electrostatic bending rigidity and electrostatically excluded volume to the stretched de Gennes-Pincus-Velasco-Brochard polyelectrolyte blob chain. A linear or sublinear dependence of the persistence length on the screening length can be ruled out. We show that previous results pointing into this direction are due to a combination of excluded-volume and finite chain length effects. The paper emphasizes the role of scaling arguments in the development of useful representations for experimental and simulation data. Received 12 February 2002     

Dynamics of strongly entangled polymer systems: activated reptation

The effect of excluded-volume interactions on the reptation dynamics of long polymer chains is considered theoretically. It is shown that interactions give rise to an exponential increase of the reptation time, , if polymer chains are long enough: , where is the number of monomers per entanglement. We propose a novel dynamical mechanism of activated reptation implying that neighboring chains exchange conformations of their terminal fragments. It is shown that the exchange mechanism is compatible with the equilibrium polymer chain statistics and that it provides a bridge between the previous theories. Received: 25 July 1997 / Accepted: 8 October 1997     

Stochastic Event-Driven Molecular Dynamics

A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. SEDMD combines event-driven molecular dynamics (EDMD) with the Direct Simulation Monte Carlo (DSMC) method. The polymers are represented as chains of hard-spheres tethered by square wells and interact with the solvent particles with hard-core potentials. The algorithm uses EDMD for the simulation of the polymer chain and the interactions between the chain beads and the surrounding solvent particles. The interactions between the solvent particles themselves are not treated deterministically as in EDMD, rather, the momentum and energy exchange in the solvent is determined stochastically using DSMC. The coupling between the solvent and the solute is consistently represented at the particle level retaining hydrodynamic interactions and thermodynamic fluctuations. However, unlike full MD simulations of both the solvent and the solute, in SEDMD the spatial structure of the solvent is ignored. The SEDMD algorithm is described in detail and applied to the study of the dynamics of a polymer chain tethered to a hard-wall subjected to uniform shear. SEDMD closely reproduces results obtained using traditional EDMD simulations with two orders of magnitude greater efficiency. Results question the existence of periodic (cycling) motion of the polymer chain.     

Hydrodynamic screening of star polymers in shear flow

The mutual effects of the conformations of a star polymer in simple shear flow and the deformation of the solvent flow field are investigated by a hybrid mesoscale simulation technique. We characterize the flow field near the star polymer as a function of its functionality (arm number) f . A strong screening of the imposed flow is found inside the star polymer, which increases with increasing f . To elucidate the importance of hydrodynamic screening, we compare results for hydrodynamic and random solvents. The dependence of the polymer orientation angle on the Weissenberg number shows a power law behavior with super-universal exponent --independent of hydrodynamic and excluded-volume interactions. In contrast, the polymer rotation frequency changes qualitatively when hydrodynamic interactions are switched on.     

Static Rouse modes and related quantities: Corrections to chain ideality in polymer melts

Following the Flory ideality hypothesis intrachain and interchain excluded-volume interactions are supposed to compensate each other in dense polymer systems. Multichain effects should thus be neglected and polymer conformations may be understood from simple phantom chain models. Here we provide evidence against this phantom chain, mean-field picture. We analyze numerically and theoretically the static correlation function of the Rouse modes. Our numerical results are obtained from computer simulations of two coarse-grained polymer models for which the strength of the monomer repulsion can be varied, from full excluded volume ("hard monomers") to no excluded volume ("phantom chains"). For nonvanishing excluded volume we find the simulated correlation function of the Rouse modes to deviate markedly from the predictions of phantom chain models. This demonstrates that there are nonnegligible correlations along the chains in a melt. These correlations can be taken into account by perturbation theory. Our simulation results are in good agreement with these new theoretical predictions.     

Melting and unzipping of DNA

Existing experimental studies of the thermal denaturation of DNA yield sharp steps in the melting curve suggesting that the melting transition is first order. This transition has been theoretically studied since the early sixties, mostly within an approach in which the microscopic configurations of a DNA molecule consist of an alternating sequence of non-interacting bound segments and denaturated loops. Studies of these models neglect the repulsive, self-avoiding, interaction between different loops and segments and have invariably yielded continuous denaturation transitions. In the present study we take into account in an approximate way the excluded-volume interaction between denaturated loops and the rest of the chain. This is done by exploiting recent results on scaling properties of polymer networks of arbitrary topology. We also ignore the heterogeneity of the polymer. We obtain a first-order melting transition in d = 2 dimensions and above, consistent with the experimental results. We also consider within our approach the unzipping transition, which takes place when the two DNA strands are pulled apart by an external force acting on one end. We find that the under equilibrium condition the unzipping transition is also first order. Although the denaturation and unzipping transitions are thermodynamically first order, they do exhibit critical fluctuations in some of their properties. For instance, the loop size distribution decays algebraically at the transition and the length of the denaturated end segment diverges as the transition is approached. We evaluate these critical properties within our approach. Received 21 August 2001 and Received in final form 26 January 2002     

Film thickness effects on the distribution of high-molecular-weight heterotelechelic polymers

High-molecular-weight heterotelechelic deuteriopolystyrene, NDPSF, possessing an amine functional group at one end of the chain and a fluorocarbon group at the other was tethered to a silicon substrate by its amine functional group. These layers were coated with an unfunctionalised polystyrene matrix, HPS, such that the total film thickness covered a range from 2.2 to 9 times the radius of gyration of NDPSF. The detailed distribution of the polymers after annealing for times much greater than the reptation period of either of the components, was obtained using neutron reflectometry. No evidence for bridging of the two interfaces was found for the thicker films, but the finite concentration of the NDPSF polymer observed for the thinnest films may be due to bridging since the energy gain of the fluorocarbon end is just greater than the loss due to configurational entropy losses. A linear increase in the ellipsometric thickness of the excess of NDPSF at the substrate was discovered and we attribute this to the NDPSF slowly being leached out of the layer initially at the substrate followed by diffusion into the bulk of the film. The concentration profiles obtained are consistent with hindered relaxation of the large NDPSF molecules, when they are tethered at the substrate or at the vacuum surface. Received 21 August 2001 and Received in final form 7 January 2002     

Molecular dynamics study of tethered polymers in shear flow

Single macromolecules can now be isolated and characterized experimentally using techniques such as optical tweezers and videomicroscopy. An interesting and important single-molecule problem is that of the dynamics of a polymer chain tethered to a solid surface and subjected to a shear flow. An experimental study of such a system was reported by Doyle et al. (Phys. Rev. Lett. 84, 4769 (2000)), and their results showed a surprising recirculating motion of the DNA chain. We explore this problem using molecular dynamics computer simulations with explicit hydrodynamic interactions. The dynamical properties of a Freely Jointed Chain (FJC) with Finitely Extensible Nonlinear Elastic (FENE) links are examined in similar conditions (i.e., confined between two surfaces and in the presence of a Poiseuille flow). We see the remarkable cyclic polymer motion observed experimentally, and we show that a simple cross-correlation function can be used to measure the corresponding period of motion. We also propose a new empirical equation relating the magnitude of the shear flow to the amount of chain deformation, an equation that appears to apply for both weak and strong flows. Finally, we report on packing effects near the molecularly flat wall, an associated chain-sticking phenomenon, and the impact of the chain hydrodynamic drag on the local fluid flow.     

Drift of a polymer chain in a porous medium --A Monte Carlo study

We investigate the drift of an end-labeled telehelic polymer chain in a frozen disordered medium under the action of a constant force applied to the one end of the macromolecule by means of an off-lattice bead spring Monte Carlo model. The length of the polymers N is varied in the range 8 < N < 128, and the obstacle concentration in the medium C is varied from zero up to the percolation threshold C≈ 0.75. For field intensities below a C-dependent critical field strength B _c, where jamming effects become dominant, we find that the conformational properties of the drifting chains can be interpreted as described by a scaling theory based on Pincus blobs. The variation of drag velocity with C in this interval of field intensities is qualitatively described by the law of Mackie-Meares. The threshold field intensity B _c itself is found to decrease linearly with C. Received 20 August 2001 and Received in final form 19 November 2001     

Multicanonical Monte Carlo simulations on intramolecular micelle formation in copolymers

The formation of intramolecular micelles in copolymers with periodic sequence, where hydrophobic units (stickers) are periodically placed along the chain, is studied by using multicanonical Monte Carlo computer simulations for an off-lattice bead-rod model in three dimensions. With decreasing the temperature, a transition from random-coil conformations to micelles occurs and flower-type micelles are formed via the transition. The number of stickers forming a micelle core is limited by the excluded-volume effect of loop chains around micelle cores. By this effect, two intramolecular micelles are formed for long polymer chains with 60 bonds via the coil-to-micelle transition. By further decreasing the temperature, we find that another transition, i.e., a micelle-to-micelle transition, takes place. At this transition point, the two intramolecular micelles merge into one micelle. Furthermore, we extend the multicanonical MC method to study elastic properties of single polymer chains with strong attractive interactions under external force fields, and study how the intramolecular micellization affects the elastic property of single polymer chains.     

Weak violation of universality for polyelectrolyte chains: Variational theory and simulations

A variational approach is considered to calculate the free energy and the conformational properties of a polyelectrolyte chain in d dimensions. We consider in detail the case of pure Coulombic interactions between the monomers, when screening is not present, in order to compute the end-to-end distance and the asymptotic properties of the chain as a function of the polymer chain length N. We find R≃N ^ν(log N)^γ, where ν = and λ is the exponent which characterizes the long-range interaction U∝ 1/r ^λ. The exponent γ is shown to be non-universal, depending on the strength of the Coulomb interaction. We check our findings by a direct numerical minimization of the variational energy for chains of increasing size 2⁴ < N < 2¹⁵. The electrostatic blob picture, expected for small enough values of the interaction strength, is quantitatively described by the variational approach. We perform a Monte Carlo simulation for chains of length 2⁴ < N < 2¹⁰. The non-universal behavior of the exponent γ previously derived within the variational method is also confirmed by the simulation results. Non-universal behavior is found for a polyelectrolyte chain in d = 3 dimension. Particular attention is devoted to the homopolymer chain problem, when short-range contact interactions are present. Received 8 August 2000 and Received in final form 19 December 2000     

Extensive stretch of polysiloxane network chains with random- and super-coiled conformations

The stress-elongation relations at large deformations for the polymer network chains with randomcoiled and supercoiled conformations are investigated using the polysiloxane networks with high elongations at break far over 10. Supercoil is the conformation of network chains in deswollen polymer networks which are made by removing solvent from the networks crosslinked in solutions at low polymer concentrations. The validity of the scaling concept of Pincus blob for the mechanical response of a polymer chain is experimentally confirmed for the network composed of randomcoiled chains. The analysis of the stress- relations for the deswollen networks comprised of supercoiled chains on the basis of the Pincus blob concept suggests that supercoil is a much more contracted conformation relative to randomcoil. Received: 25 August 1997 / Received in final form: 13 October 1997 / Accepted: 22 January 1998     

Polyelectrolyte chains in poor solvent. A variational description of necklace formation

We study the properties of polyelectrolyte chains under different solvent conditions, using a variational technique. The free energy and the conformational properties of a polyelectrolyte chain are studied by minimizing the free energy F_N, depending on N(N - 1)/2 trial probabilities that characterize the conformation of the chain. The Gaussian approximation is considered for a ring of length 2⁴ < N < 2⁸ and for an open chain of length 50 < N < 200 in poor- and theta-solvent conditions, including a Coulomb repulsion between the monomers. In theta-solvent conditions the blob size is measured and found in agreement with scaling theory, including charge depletion effects, expected for the case of an open chain. In poor-solvent conditions, a globule instability, driven by electrostatic repulsion, is observed. We notice also inhomogeneous behavior of the monomer-monomer correlation function, reminiscence of necklace formation in poor-solvent polyelectrolyte solutions. A global phase diagram in terms of solvent quality and inverse Bjerrum length is presented. Received 7 June 2001 and Received in final form 17 October 2001     

Some relevant parameters affecting the glass transition of supported ultra-thin polymer films

We have measured, the thickness dependence of the glass transition temperature T(g)( h), using ellipsometry at variable temperature, for poly(methyl-methacrylate) (PMMA) of various tacticity in confined geometry. We report that several factors significantly affect T(g)( h): i) polymer microstructure (stereoregularity of PMMA) related to local dynamics; ii) interfacial interactions; iii) conformation of the polymer chains. These results raise many fundamental questions on the origin of the thickness-dependent glass transition. Why and how do the interactions with the substrate significantly affect T(g)( h)? Does T(g)( h) depend on the modifications of conformational parameters of the chains (their entropy)? What is the correlation between local dynamics and T(g)( h) in thin films? The aim of this paper is to summarise these open questions, which should stimulate further investigations in the thin polymer film scientific community.     

Force-extension behavior of folding polymers

The elastic response of flexible polymers made of elements which can be either folded or unfolded, having different lengths in these two states, is discussed. These situations are common for biopolymers as a result of folding interactions intrinsic to the monomers, or as a result of binding of other smaller molecules along the polymer length. Using simple flexible-chain models, we show that even when the energy ε associated with maintaining the folded state is comparable to k _B T, the elastic response of such a chain can mimic usual polymer linear elasticity, but with a force scale enhanced above that expected from the flexibility of the chain backbone. We discuss recent experiments on single-stranded DNA, chromatin fiber and double-stranded DNA with proteins weakly absorbed along its length which show this effect. Effects of polymer semiflexiblity and torsional stiffness relevant to experiments on proteins binding to dsDNA are analyzed. We finally discuss the competition between electrostatic self-repulsion and folding interactions responsible for the complex elastic response of single-stranded DNA. Received 7 August 2002 and Received in final form 7 March 2003 / Published online: 15 April 2003 RID="a" ID="a"e-mail: jmarko@uic.edu     

A FT-IR absorption analysis of vibrational properties of water encaged in NaA zeolites: evidence of a “structure maker” role of zeolitic surface

Linear polyisoprenes having dimethylamine end groups were prepared by high vacuum anionic polymerization techniques using 3-dimethylaminopropyllithium as the initiator. The amine group was reacted with 2-cholesteryl-2-oxo-1,3,2-dioxaphospholane to provide polymer chains having end zwitterionic groups chemically connected with cholesterol. The association behavior of these end-functionalized polymers was studied in cyclohexane by low angle laser light scattering, dynamic light scattering, and viscometry. The aggregation numbers, N _w were found to decrease by increasing the molecular weight of the precursor polymer, due to excluded volume repulsions. The ability of cholesterol to form liquid crystal mesophases facilitated the association process leading to higher N _w values. The hydrodynamic behavior of the aggregates was similar to that of star polymers. The dependence of the N _w values on the molecular weight of the base polymer, the polydispersity of the associates and the absence of critical micelle concentration, cmc are compatible with the linear head-packing model. Received 29 April 2002 and Received in final form 13 November 2002 Published online: 11 March 2003     

Molecular Dynamics simulation of a polymer chain translocating through a nanoscopic pore

The detection of linear polymers translocating through a nanoscopic pore is a promising idea for the development of new DNA analysis techniques. However, the physics of constrained macromolecules and the fluid that surrounds them at the nanoscopic scale is still not well understood. In fact, many theoretical models of polymer translocation neglect both excluded-volume and hydrodynamic effects. We use Molecular Dynamics simulations with explicit solvent to study the impact of hydrodynamic interactions on the translocation time of a polymer. The translocation time τ that we examine is the unbiased (no charge on the chain and no driving force) escape time of a polymer that is initially placed halfway through a pore perforated in a monolayer wall. In particular, we look at the effect of increasing the pore radius when only a small number of fluid particles can be located in the pore as the polymer undergoes translocation, and we compare our results to the theoretical predictions of Chuang et al. (Phys. Rev. E 65, 011802 (2001)). We observe that the scaling of the translocation time varies from τ ∼ N ^11/5 to τ ∼ N ^9/5 as the pore size increases (N is the number of monomers that goes up to 31 monomers). However, the scaling of the polymer relaxation time remains consistent with the 9/5 power law for all pore radii.     

Polymers with self-avoiding interaction in random medium: a localization-delocalization transition

In this paper we investigate the problem of a long self-avoiding polymer chain immersed in a random medium. We find that in the limit of a very long chain and when the self-avoiding interaction is weak, the conformation of the chain consists of many “blobs” with connecting segments. The blobs are sections of the molecule curled up in regions of low potential in the case of a Gaussian distributed random potential or in regions of relatively low density of obstacles in the case of randomly distributed hard obstacles. We find that as the strength of the self-avoiding interaction is increased the chain undergoes a delocalization transition in the sense that the appropriate free energy per monomer is no longer negative. The chain is then no longer bound to a particular location in the medium but can easily wander around under the influence of a small perturbation. For a localized chain we estimate quantitatively the expected number of monomers in the “blobs” and in the connecting segments. Received 13 November 2002 Published online 14 March 2003     

Mobility in thin polymer films ranging from local segmental motion, Rouse modes to whole chain motion: A coupling model consideration

Large increases of mobility of local segmental relaxation observed in polymer films as the film thickness is decreased, as evidenced by decreases of the glass temperature, are not found for relaxation mechanisms that have longer length scales including the Rouse relaxation modes and the diffusion of entire polymer chains. We show that the coupling model predictions, when extended to consider polymer thin films, are consistent with a large increase of the mobility of the local segmental motions and the lack of such a change for the Rouse modes and the diffusion of entire polymer chains. There are two effects that can reduce the coupling parameter of the local segmental relaxation in thin films. One is the chain orientation that is induced parallel to the surface when the film thickness h becomes smaller than the end-to-end distance of the chains and the other is a finite-size effect when h is no longer large compared to the cooperative length scale. Extremely thin ( ≈ 1.5 nm) films obtained by intercalating a polymer into layered silicates have thickness significantly less than the cooperative length scale near the bulk polymer glass transition temperature. As a result, the coupling parameter of the local segmental relaxation in such thin films is reduced almost to zero. With this plausible assumption, we show the coupling model can explain quantitatively the large decrease of the local segmental relaxation time found experimentally. Received 1 August 2001 and Received in final form 1 December 2001