Strain-dependent localization, microscopic deformations, and macroscopic normal tensions in model polymer networks

We use molecular dynamics simulations to investigate the microscopic and macroscopic response of model polymer networks to uniaxial elongations. By studying networks with strands lengths ranging from $N_s=20$ to 200 we cover the full crossover from cross-link to entanglement dominated behavior. Our results support a recent version of the tube model which accounts for the different strain dependence of chain localization due to chemical cross-links and entanglements

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 \DH intrachain interactions in the limit where the screening length $\kappa^{-1}$ 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 $l_e\propto\kappa^{-2}$ by Khokhlov and Khachaturian which is based on applying the Odijk-Skolnick-Fixman theory 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 argue that previous numerical results pointing into this direction are probably 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.Comment: 11 pages, 7 figure

Self-similar chain conformations in polymer gels

We use molecular dynamics simulations to study the swelling of randomly end-cross-linked polymer networks in good solvent conditions. We find that the equilibrium degree of swelling saturates at Q_eq = N_e**(3/5) for mean strand lengths N_s exceeding the melt entanglement length N_e. The internal structure of the network strands in the swollen state is characterized by a new exponent nu=0.72. Our findings are in contradiction to de Gennes' c*-theorem, which predicts Q_eq proportional N_s**(4/5) and nu=0.588. We present a simple Flory argument for a self-similar structure of mutually interpenetrating network strands, which yields nu=7/10 and otherwise recovers the classical Flory-Rehner theory. In particular, Q_eq = N_e**(3/5), if N_e is used as effective strand length.Comment: 4 pages, RevTex, 3 Figure

Simulating Van der Waals-interactions in water/hydrocarbon-based complex fluids

In systems composed of water and hydrocarbons Van der Waals-interactions are dominated by the non-retarded, classical (Keesom) part of the Lifshitz-interaction; the interaction is screened by salt and extends over mesoscopic distances of the order of the size of the (micellar) constituents of complex fluids. We show that these interactions are included intrinsically in a recently introduced local Monte Carlo algorithm for simulating electrostatic interactions between charges in the presence of non-homogeneous dielectric media

Stress Relaxation of Entangled Polymer Networks

The non-linear stress-strain relation for crosslinked polymer networks is studied using molecular dynamics simulations. Previously we demonstrated the importance of trapped entanglements in determining the elastic and relaxational properties of networks. Here we present new results for the stress versus strain for both dry and swollen networks. Models which limit the fluctuations of the network strands like the tube model are shown to describe the stress for both elongation and compression. For swollen networks, the total modulus is found to decrease like (V_0/V)^{2/3} and goes to the phantom model result only for short strand networks.Comment: 9 pages, 3 figures, RevTe

DNA nano-mechanics: how proteins deform the double helix

It is a standard exercise in mechanical engineering to infer the external forces and torques on a body from its static shape and known elastic properties. Here we apply this kind of analysis to distorted double-helical DNA in complexes with proteins. We extract the local mean forces and torques acting on each base-pair of bound DNA from high-resolution complex structures. Our method relies on known elastic potentials and a careful choice of coordinates of the well-established rigid base-pair model of DNA. The results are robust with respect to parameter and conformation uncertainty. They reveal the complex nano-mechanical patterns of interaction between proteins and DNA. Being non-trivially and non-locally related to observed DNA conformations, base-pair forces and torques provide a new view on DNA-protein binding that complements structural analysis.Comment: accepted for publication in JCP; some minor changes in response to review 18 pages, 5 figure + supplement: 4 pages, 3 figure

Multi-scale modeling of diffusion-controlled reactions in polymers: Renormalisation of reactivity parameters

The quantitative description of polymeric systems requires hierarchical modeling schemes, which bridge the gap between the atomic scale, relevant to chemical or biomolecular reactions, and the macromolecular scale, where the longest relaxation modes occur. Here, we use the formalism for diffusion-controlled reactions in polymers developed by Wilemski, Fixman, and Doi to discuss the renormalisation of the reactivity parameters in polymer models with varying spatial resolution. In particular, we show that the adjustments are independent of chain length. As a consequence, it is possible to match reactions times between descriptions with different resolution for relatively short reference chains and to use the coarse-grained model to make quantitative predictions for longer chains. We illustrate our results by a detailed discussion of the classical problem of chain cyclization in the Rouse model, which offers the simplest example of a multi-scale descriptions, if we consider differently discretized Rouse models for the same physical system. Moreover, we are able to explore different combinations of compact and non-compact diffusion in the local and large-scale dynamics by varying the embedding dimension. Z9

Topological versus rheological entanglement length in primitive path analysis protocols

Primitive path analysis algorithms are now routinely employed to analyze entanglements in computer simulations of polymeric systems, but different analysis protocols result in different estimates of the entanglement length, N_e. Here we argue that standard PPA measures the rheological entanglement length, typically employed by tube models and relevant to quantitative comparisons with experiment, while codes like Z or CReTA also determine the topological entanglement length. For loosely entangled systems, a simple analogy between between phantom networks and the mesh of entangled primitive paths suggests a factor of two between the two numbers. This result is in excellent agreement with reported values for poly-ethylene, poly-butadiene and bead-spring polymer melts.Comment: 3 pages, no figure