Protein-Mediated DNA Loops: Effects of Protein Bridge Size and Kinks

This paper focuses on the probability that a portion of DNA closes on itself through thermal fluctuations. We investigate the dependence of this probability upon the size r of a protein bridge and/or the presence of a kink at half DNA length. The DNA is modeled by the Worm-Like Chain model, and the probability of loop formation is calculated in two ways: exact numerical evaluation of the constrained path integral and the extension of the Shimada and Yamakawa saddle point approximation. For example, we find that the looping free energy of a 100 base pairs DNA decreases from 24 kT to 13 kT when the loop is closed by a protein of r = 10 nm length. It further decreases to 5 kT when the loop has a kink of 120 degrees at half-length.Comment: corrected typos and figures, references updated; 13 pages, 7 figures, accepted for publication in Phys. Rev.

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

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

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

Fluctuating semiflexible polymer ribbon constrained to a ring

Twist stiffness and an asymmetric bending stiffness of a polymer or a polymer bundle is captured by the elastic ribbon model. We investigate the effects a ring geometry induces to a thermally fluctuating ribbon, finding bend-bend coupling in addition to twist-bend coupling. Furthermore, due to the geometric constraint the polymer's effective bending stiffness increases. A new parameter for experimental investigations of polymer bundles is proposed: the mean square diameter of a ribbonlike ring, which is determined analytically in the semiflexible limit. Monte Carlo simulations are performed which affirm the model's prediction up to high flexibility.Comment: 6 pages, 3 figures, Version as published in Eur. Phys. J.

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

Influence of the structural modulations and the Chain-ladder interaction in the Sr_14−xCa_xCu_24O_41Sr\_{14-x}Ca\_{x}Cu\_{24}O\_{41} compounds

We studied the effects of the incommensurate structural modulations on the ladder subsystem of the $Sr\_{14-x}Ca\_{x}Cu\_{24}O\_{41}$ family of compounds using ab-initio explicitly-correlated calculations. From these calculations we derived $t-J$ model as a function of the fourth crystallographic coordinate $\tau$ describing the incommensurate modulations. It was found that in the highly calcium-doped system, the on-site orbital energies are strongly modulated along the ladder legs. On the contrary the two sites of the ladder rungs are iso-energetic and the holes are thus expected to be delocalized on the rungs. Chain-ladder interactions were also evaluated and found to be very negligible. The ladder superconductivity model for these systems is discussed in the light of the present results.Comment: 8 octobre 200

Bimodal distribution function of a 3d wormlike chain with a fixed orientation of one end

We study the distribution function of the three dimensional wormlike chain with a fixed orientation of one chain end using the exact representation of the distribution function in terms of the Green's function of the quantum rigid rotator in a homogeneous external field. The transverse 1d distribution function of the free chain end displays a bimodal shape in the intermediate range of the chain lengths ($1.3L_{p},...,3.5L_{p}$). We present also analytical results for short and long chains, which are in complete agreement with the results of previous studies obtained using different methods.Comment: 6 pages, 3 figure