Calculation of the persistence length of a flexible polymer chain with short range self-repulsion

For a self-repelling polymer chain consisting of n segments we calculate the persistence length L(j,n), defined as the projection of the end-to-end vector on the direction of the j`th segment. This quantity shows some pronounced variation along the chain. Using the renormalization group and epsilon-expansion we establish the scaling form and calculate the scaling function to order epsilon^2. Asymptotically the simple result L(j,n) ~ const(j(n-j)/n)^(2nu-1) emerges for dimension d=3. Also outside the excluded volume limit L(j,n) is found to behave very similar to the swelling factor of a chain of length j(n-j)/n. We carry through simulations which are found to be in good accord with our analytical results. For d=2 both our and previous simulations as well as theoretical arguments suggest the existence of logarithmic anomalies.Comment: 28 pages, 8 figures, changed conten

Lattice Kinetics of Diffusion-Limited Coalescence and Annihilation with Sources

We study the 1D kinetics of diffusion-limited coalescence and annihilation with back reactions and different kinds of particle input. By considering the changes in occupation and parity of a given interval, we derive sets of hierarchical equations from which exact expressions for the lattice coverage and the particle concentration can be obtained. We compare the mean-field approximation and the continuum approximation to the exact solutions and we discuss their regime of validity.Comment: 24 pages and 3 eps figures, Revtex, accepted for publication in J. Phys.

Structure of Polyelectrolytes in Poor Solvent

We present simulations on charged polymers in poor solvent. First we investigate in detail the dilute concentration range with and without imposed extension constraints. The resulting necklace polymer conformations are analyzed in detail. We find strong fluctuations in the number of pearls and their sizes leading only to small signatures in the form factor and the force-extension relation. The scaling of the peak in the structure factor with the monomer density shows a pertinent different behavior from good solvent chains.Comment: 7 pages, 5 figures. submitted to EP

The scaling behaviour of screened polyelectrolytes

We present a field-theoretic renormalization group (RG) analysis of a single flexible, screened polyelectrolyte chain (a Debye-H\"uckel chain) in a polar solvent. We point out that the Debye-H\"uckel chain may be mapped onto a local field theory which has the same fixed point as a generalised $n \to 1$ Potts model. Systematic analysis of the field theory shows that the system is one with two interplaying length-scales requiring the calculation of scaling functions as well as exponents to fully describe its physical behaviour. To illustrate this, we solve the RG equation and explicitly calculate the exponents and the mean end-to-end length of the chain.Comment: 6 pages, 1 figure; changed title and slight modification to tex

The Transcriptional Regulator Rok Binds A+T-Rich DNA and Is Involved in Repression of a Mobile Genetic Element in Bacillus subtilis

The rok gene of Bacillus subtilis was identified as a negative regulator of competence development. It also controls expression of several genes not related to competence. We found that Rok binds to extended regions of the B. subtilis genome. These regions are characterized by a high A+T content and are known or believed to have been acquired by horizontal gene transfer. Some of the Rok binding regions are in known mobile genetic elements. A deletion of rok resulted in higher excision of one such element, ICEBs1, a conjugative transposon found integrated in the B. subtilis genome. When expressed in the Gram negative E. coli, Rok also associated with A+T-rich DNA and a conserved C-terminal region of Rok contributed to this association. Together with previous work, our findings indicate that Rok is a nucleoid associated protein that serves to help repress expression of A+T-rich genes, many of which appear to have been acquired by horizontal gene transfer. In these ways, Rok appears to be functionally analogous to H-NS, a nucleoid associated protein found in Gram negative bacteria and Lsr2 of high G+C Mycobacteria

Unified Homogenization Theory for Magnetoinductive and Electromagnetic Waves in Split Ring Metamaterials

A unified homogenization procedure for split ring metamaterials taking into account time and spatial dispersion is introduced. The procedure is based on two coupled systems of equations. The first one comes from an approximation of the metamaterial as a cubic arrangement of coupled LC circuits, giving the relation between currents and local magnetic field. The second equation comes from macroscopic Maxwell equations, and gives the relation between the macroscopic magnetic field and the average magnetization of the metamaterial. It is shown that electromagnetic and magnetoinductive waves propagating in the metamaterial are obtained from this analysis. Therefore, the proposed time and spatially dispersive permeability accounts for the characterization of the complete spectrum of waves of the metamaterial. Finally, it is shown that the proposed theory is in good quantitative and qualitative agreement with full wave simulations.Comment: 4 pages, 3 figure

A Modified Random Phase Approximation of Polyelectrolyte Solutions

We compute the phase diagram of salt-free polyelectrolyte solutions using a modified Debye-Huckel Approach. We introduce the chain connectivity via the Random Phase Approximation with two important modifications. We modify the electrostatic potential at short distances to include a bound on the electrostatic attractions at the distance of closest approach between charges. This modification is shown to act as a hard core in the phase diagram of electrolyte solutions. We also introduce a cut-off on the integration of the modes of wave length smaller than the size over which the chains are strongly perturbed by the electrostatic interactions. This cut-off is shown to be essential to predict physical phase diagram in long chain solutions