Anisotropic Random Networks of Semiflexible Polymers

Motivated by the organization of crosslinked cytoskeletal biopolymers, we present a semimicroscopic replica field theory for the formation of anisotropic random networks of semiflexible polymers. The networks are formed by introducing random permanent crosslinks which fix the orientations of the corresponding polymer segments to align with one another. Upon increasing the crosslink density, we obtain a continuous gelation transition from a fluid phase to a gel where a finite fraction of the system gets localized at random positions. For sufficiently stiff polymers, this positional localization is accompanied by a {\em continuous} isotropic-to-nematic (IN) transition occuring at the same crosslink density. As the polymer stiffness decreases, the IN transition becomes first order, shifts to a higher crosslink density, and is preceeded by an orientational glass (statistically isotropic amorphous solid) where the average polymer orientations freeze in random directions.Comment: 5 pages, 2 figures; final version with expanded discussion to appear in PR

Linear response of a grafted semiflexible polymer to a uniform force field

We use the worm-like chain model to analytically calculate the linear response of a grafted semiflexible polymer to a uniform force field. The result is a function of the bending stiffness, the temperature, the total contour length, and the orientation of the field with respect to that of the grafted end. We also study the linear response of a worm-like chain with a periodic alternating sequence of positive and negative charges. This can be considered as a model for a polyampholyte with intrinsic bending siffness and negligible intramolecular interactions. We show how the finite intrinsic persistence length affects the linear response to the external field.Comment: 6 pages, 3 figure

Fluctuation-Dissipation Theorem for the Microcanonical Ensemble

A derivation of the Fluctuation-Dissipation Theorem for the microcanonical ensemble is presented using linear response theory. The theorem is stated as a relation between the frequency spectra of the symmetric correlation and response functions. When the system is not in the thermodinamic limit, this result can be viewed as an extension of the fluctuation-dissipation relations to a situation where dynamical fluctuations determine the response. Therefore, the relation presented here between equilibrium fluctuations and response can have a very different physical nature from the usual one in the canonical ensemble. These considerations imply that the Fluctuation-Dissipation Theorem is not restricted to the context of thermal equilibrium, where it is usually derived. Dispersion relations and sum rules are also obtained and discussed in the present case. Although analogous to the Kramers-Kronig relations, they are not related to the frequency spectrum but to the energy dependence of the response function.Comment: 15 pages, v3: final version, new text added, new reference

Conformations of confined biopolymers

Nanoscale and microscale confinement of biopolymers naturally occurs in cells and has been recently achieved in artificial structures designed for nanotechnological applications. Here, we present an extensive theoretical investigation of the conformations and shape of a biopolymer with varying stiffness confined to a narrow channel. Combining scaling arguments, analytical calculations, and Monte Carlo simulations, we identify various scaling regimes where master curves quantify the functional dependence of the polymer conformations on the chain stiffness and strength of confinement.Comment: 5 pages, 4 figures, minor correction

New Universality of Lyapunov Spectra in Hamiltonian Systems

A new universality of Lyapunov spectra {\lambda_i} is shown for Hamiltonian systems. The universality appears in middle energy regime and is different from another universality which can be reproduced by random matrices in the following two points. One is that the new universality appears in a limited range of large i/N rather than the whole range, where N is degrees of freedom. The other is Lyapunov spectra do not behave linearly while random matrices give linear behavior even on 3D lattice. Quadratic terms with smaller nonlinear terms of potential functions play an intrinsic role in the new universality.Comment: 19 pages, 16 Encapsulated Postscript figures, LaTeX (100 kb

Tension dynamics in semiflexible polymers. Part I: Coarse-grained equations of motion

Based on the wormlike chain model, a coarse-grained description of the nonlinear dynamics of a weakly bending semiflexible polymer is developed. By means of a multiple scale perturbation analysis, a length-scale separation inherent to the weakly-bending limit is exploited to reveal the deterministic nature of the spatio-temporal relaxation of the backbone tension and to deduce the corresponding coarse-grained equation of motion. From this partial integro-differential equation, some detailed analytical predictions for the non-linear response of a weakly bending polymer are derived in an accompanying paper (Part II, cond-mat/0609638).Comment: 14 pages, 4 figyres. The second part of this article has the preprint no.: cond-mat/060963

Transverse fluctuations of grafted polymers

We study the statistical mechanics of grafted polymers of arbitrary stiffness in a two-dimensional embedding space with Monte Carlo simulations. The probability distribution function of the free end is found to be highly anisotropic and non-Gaussian for typical semiflexible polymers. The reduced distribution in the transverse direction, a Gaussian in the stiff and flexible limits, shows a double peak structure at intermediate stiffnesses. We also explore the response to a transverse force applied at the polymer free end. We identify F-Actin as an ideal benchmark for the effects discussed.Comment: 10 pages, 4 figures, submitted to Physical Review