Facilitated diffusion of DNA-binding proteins

The diffusion-controlled limit of reaction times for site-specific DNA-binding proteins is derived from first principles. We follow the generally accepted concept that a protein propagates via two competitive modes, a three-dimensional diffusion in space and a one-dimensional sliding along the DNA. However, our theoretical treatment of the problem is new. The accuracy of our analytical model is verified by numerical simulations. The results confirm that the unspecific binding of protein to DNA, combined with sliding, is capable to reduce the reaction times significantly.Comment: 4 pages, 2 figures Nov 22 2005 - accepted for PR

Multiscale entanglement in ring polymers under spherical confinement

The interplay of geometrical and topological entanglement in semiflexible knotted polymer rings confined inside a spherical cavity is investigated using advanced numerical methods. By using stringent and robust algorithms for locating knots, we characterize how the knot length lk depends on the ring contour length, Lc and the radius of the confining sphere, Rc . In the no- and strong- confinement cases we observe weak knot localization and complete knot delocalization, respectively. We show that the complex interplay of lk, Lc and Rc that seamlessly bridges these two limits can be encompassed by a simple scaling argument based on deflection theory. The same argument is used to rationalize the multiscale character of the entanglement that emerges with increasing confinement.Comment: 9 pages 9 figure

The two-angle model and the phase diagram for Chromatin

We have studied the phase diagram for chromatin within the framework of the two-angle model. Rather than improving existing models with finer details our main focus of the work is getting mathematically rigorous results on the structure, especially on the excluded volume effects and the effects on the energy due to the long-range forces and their screening. Thus we present a phase diagram for the allowed conformations and the Coulomb energies

Scattering functions of knotted ring polymers

We discuss the scattering function of a Gaussian random polygon with N nodes under a given topological constraint through simulation. We obtain the Kratky plot of a Gaussian polygon of N=200 having a fixed knot for some different knots such as the trivial, trefoil and figure-eight knots. We find that some characteristic properties of the different Kratky plots are consistent with the distinct values of the mean square radius of gyration for Gaussian polygons with the different knots.Comment: 4pages, 3figures, 3table

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.

Modeling Bacterial DNA: Simulation of Self-avoiding Supercoiled Worm-Like Chains Including Structural Transitions of the Helix

Under supercoiling constraints, naked DNA, such as a large part of bacterial DNA, folds into braided structures called plectonemes. The double-helix can also undergo local structural transitions, leading to the formation of denaturation bubbles and other alternative structures. Various polymer models have been developed to capture these properties, with Monte-Carlo (MC) approaches dedicated to the inference of thermodynamic properties. In this chapter, we explain how to perform such Monte-Carlo simulations, following two objectives. On one hand, we present the self-avoiding supercoiled Worm-Like Chain (ssWLC) model, which is known to capture the folding properties of supercoiled DNA, and provide a detailed explanation of a standard MC simulation method. On the other hand, we explain how to extend this ssWLC model to include structural transitions of the helix.Comment: Book chapter to appear in The Bacterial Nucleoid, Methods and Protocols, Springer serie

On the Limits of Analogy Between Self-Avoidance and Topology-Driven Swelling of Polymer Loops

The work addresses the analogy between trivial knotting and excluded volume in looped polymer chains of moderate length, $N<N_0$, where the effects of knotting are small. A simple expression for the swelling seen in trivially knotted loops is described and shown to agree with simulation data. Contrast between this expression and the well known expression for excluded volume polymers leads to a graphical mapping of excluded volume to trivial knots, which may be useful for understanding where the analogy between the two physical forms is valid. The work also includes description of a new method for the computational generation of polymer loops via conditional probability. Although computationally intensive, this method generates loops without statistical bias, and thus is preferable to other loop generation routines in the region $N<N_0$.Comment: 10 pages, 5 figures, supplementary tex file and datafil

Characteristic length of random knotting for cylindrical self-avoiding polygons

We discuss the probability of random knotting for a model of self-avoiding polygons whose segments are given by cylinders of unit length with radius $r$. We show numerically that the characteristic length of random knotting is roughly approximated by an exponential function of the chain thickness $r$.Comment: 5 pages, 4 figure

CRANKITE: a fast polypeptide backbone conformation sampler

Background: CRANKITE is a suite of programs for simulating backbone conformations of polypeptides and proteins. The core of the suite is an efficient Metropolis Monte Carlo sampler of backbone conformations in continuous three-dimensional space in atomic details. Methods: In contrast to other programs relying on local Metropolis moves in the space of dihedral angles, our sampler utilizes local crankshaft rotations of rigid peptide bonds in Cartesian space. Results: The sampler allows fast simulation and analysis of secondary structure formation and conformational changes for proteins of average length