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

Structure and dynamics of interphase chromosomes

During interphase chromosomes decondense, but fluorescent in situ hybridization experiments reveal the existence of distinct territories occupied by individual chromosomes inside the nuclei of most eukaryotic cells. We use computer simulations to show that the existence and stability of territories is a kinetic effect that can be explained without invoking an underlying nuclear scaffold or protein-mediated interactions between DNA sequences. In particular, we show that the experimentally observed territory shapes and spatial distances between marked chromosome sites for human, Drosophila, and budding yeast chromosomes can be reproduced by a parameter-free minimal model of decondensing chromosomes. Our results suggest that the observed interphase structure and dynamics are due to generic polymer effects: confined Brownian motion conserving the local topological state of long chain molecules and segregation of mutually unentangled chains due to topological constraint

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

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

Coarse-grained Interaction Potentials for Anisotropic Molecules

We have proposed an efficient parameterization method for a recent variant of the Gay-Berne potential for dissimilar and biaxial particles and demonstrated it for a set of small organic molecules. Compared to the previously proposed coarse-grained models, the new potential exhibits a superior performance in close contact and large distant interactions. The repercussions of thermal vibrations and elasticity has been studied through a statistical method. The study justifies that the potential of mean force is representable with the same functional form, extending the application of this coarse-grained description to a broader range of molecules. Moreover, the advantage of employing coarse-grained models over truncated atomistic summations with large distance cutoffs has been briefly studied.Comment: 8 pages, 4 tables and 6 figures. To appear in J. Chem. Phy

Simulating nanoscale dielectric response

We introduce a constrained energy functional to describe dielectric response. We demonstrate that the local functional is a generalization of the long ranged Marcus energy. Our re-formulation is used to implement a cluster Monte Carlo algorithm for the simulation of dielectric media. The algorithm avoids solving the Poisson equation and remains efficient in the presence of spatial heterogeneity, nonlinearity and scale dependent dielectric properties.Comment: 4 pages, 2 figures. Revtex