Disordered, stretched, and semiflexible biopolymers in two dimensions

We study the effects of intrinsic sequence-dependent curvature for a two dimensional semiflexible biopolymer with short-range correlation in intrinsic curvatures. We show exactly that when not subjected to any external force, such a system is equivalent to a system with a well-defined intrinsic curvature and a proper renormalized persistence length. We find the exact expression for the distribution function of the equivalent system. However, we show that such an equivalent system does not always exist for the polymer subjected to an external force. We find that under an external force, the effect of sequence-disorder depends upon the averaging order, the degree of disorder, and the experimental conditions, such as the boundary conditions. Furthermore, a short to moderate length biopolymer may be much softer or has a smaller apparent persistent length than what would be expected from the "equivalent system". Moreover, under a strong stretching force and for a long biopolymer, the sequence-disorder is immaterial for elasticity. Finally, the effect of sequence-disorder may depend upon the quantity considered

Semiflexible polymers: Dependence on ensemble and boundary orientations

We show that the mechanical properties of a worm-like-chain (WLC) polymer, of contour length $L$ and persistence length \l such that t=L/\l\sim{\cal O}(1), depend both on the ensemble and the constraint on end-orientations. In the Helmholtz ensemble, multiple minima in free energy near $t=4$ persists for all kinds of orientational boundary conditions. The qualitative features of projected probability distribution of end to end vector depend crucially on the embedding dimensions. A mapping of the WLC model, to a quantum particle moving on the surface of an unit sphere, is used to obtain the statistical and mechanical properties of the polymer under various boundary conditions and ensembles. The results show excellent agreement with Monte-Carlo simulations.Comment: 15 pages, 15 figures; version accepted for publication in Phys. Rev. E; one new figure and discussions adde

Entropic forces generated by grafted semiflexible polymers

The entropic force exerted by the Brownian fluctuations of a grafted semiflexible polymer upon a rigid smooth wall are calculated both analytically and by Monte Carlo simulations. Such forces are thought to play an important role for several cellular phenomena, in particular, the physics of actin-polymerization-driven cell motility and movement of bacteria like Listeria. In the stiff limit, where the persistence length of the polymer is larger than its contour length, we find that the entropic force shows scaling behavior. We identify the characteristic length scales and the explicit form of the scaling functions. In certain asymptotic regimes we give simple analytical expressions which describe the full results to a very high numerical accuracy. Depending on the constraints imposed on the transverse fluctuations of the filament there are characteristic differences in the functional form of the entropic forces; in a two-dimensional geometry the entropic force exhibits a marked peak.Comment: 21 pages, 18 figures, minor misprints correcte

Long Range Bond-Bond Correlations in Dense Polymer Solutions

The scaling of the bond-bond correlation function $C(s)$ along linear polymer chains is investigated with respect to the curvilinear distance, $s$, along the flexible chain and the monomer density, $\rho$, via Monte Carlo and molecular dynamics simulations. % Surprisingly, the correlations in dense three dimensional solutions are found to decay with a power law $C(s) \sim s^{-\omega}$ with $\omega=3/2$ and the exponential behavior commonly assumed is clearly ruled out for long chains. % In semidilute solutions, the density dependent scaling of $C(s) \approx g^{-\omega_0} (s/g)^{-\omega}$ with $\omega_0=2-2\nu=0.824$ ($\nu=0.588$ being Flory's exponent) is set by the number of monomers $g(\rho)$ contained in an excluded volume blob of size $\xi$. % Our computational findings compare well with simple scaling arguments and perturbation calculation. The power-law behavior is due to self-interactions of chains on distances $s \gg g$ caused by the connectivity of chains and the incompressibility of the melt. %Comment: 4 pages, 4 figure

Elasticity of semi-flexible polymers

We present a numerical solution of the Worm-Like Chain (WLC) model for semi-flexible polymers. We display graphs for the end-to-end distance distribution and the force-extension relation expected from the model. We predict the expected level of fluctuations around the mean value in force-extension curves. Our treatment analyses the entire range of polymer lengths and reproduces interesting qualitative features seen in recent computer simulations for polymers of intermediate length. These results can be tested against experiments on single molecules. This study is relevant to mechanical properties of biological molecules.Comment: five pages revtex five figures, slightly improved version with recent references adde

Statics and Dynamics of the Wormlike Bundle Model

Bundles of filamentous polymers are primary structural components of a broad range of cytoskeletal structures, and their mechanical properties play key roles in cellular functions ranging from locomotion to mechanotransduction and fertilization. We give a detailed derivation of a wormlike bundle model as a generic description for the statics and dynamics of polymer bundles consisting of semiflexible polymers interconnected by crosslinking agents. The elastic degrees of freedom include bending as well as twist deformations of the filaments and shear deformation of the crosslinks. We show that a competition between the elastic properties of the filaments and those of the crosslinks leads to renormalized effective bend and twist rigidities that become mode-number dependent. The strength and character of this dependence is found to vary with bundle architecture, such as the arrangement of filaments in the cross section and pretwist. We discuss two paradigmatic cases of bundle architecture, a uniform arrangement of filaments as found in F-actin bundles and a shell-like architecture as characteristic for microtubules. Each architecture is found to have its own universal ratio of maximal to minimal bending rigidity, independent of the specific type of crosslink induced filament coupling; our predictions are in reasonable agreement with available experimental data for microtubules. Moreover, we analyze the predictions of the wormlike bundle model for experimental observables such as the tangent-tangent correlation function and dynamic response and correlation functions. Finally, we analyze the effect of pretwist (helicity) on the mechanical properties of bundles. We predict that microtubules with different number of protofilaments should have distinct variations in their effective bending rigidity

Getting DNA twist rigidity from single molecule experiments

We use an elastic rod model with contact to study the extension versus rotation diagrams of single supercoiled DNA molecules. We reproduce quantitatively the supercoiling response of overtwisted DNA and, using experimental data, we get an estimation of the effective supercoiling radius and of the twist rigidity of B-DNA. We find that unlike the bending rigidity, the twist rigidity of DNA seems to vary widely with the nature and concentration of the salt buffer in which it is immerged

Polymer chain stiffness versus excluded volume: A Monte Carlo study of the crossover towards the wormlike chain model

When the local intrinsic stiffness of a polymer chain varies over a wide range, one can observe both a crossover from rigid-rod-like behavior to (almost) Gaussian random coils and a further crossover towards self-avoiding walks in good solvents. Using the pruned-enriched Rosenbluth method (PERM) to study self-avoiding walks of up to $N_b=50000$ steps and variable flexibility, the applicability of the Kratky-Porod model is tested. Evidence for non-exponential decay of the bond-orientational correlations $<\cos \theta (s) >$ for large distances $s$ along the chain contour is presented, irrespective of chain stiffness. For bottle-brush polymers on the other hand, where experimentally stiffness is varied via the length of side-chains, it is shown that these cylindrical brushes (with flexible backbones) are not described by the Kratky-Porod wormlike chain model, since their persistence length is (roughly) proportional to their cross-sectional radius, for all conditions of practical interest.Comment: 6 pages, 5 figures, to be published in Europhys. Lett. (2010