Electric response of DNA hairpins to magnetic fields

We study the electric properties of single-stranded DNA molecules with hairpin-like shapes in the presence of a magnetic flux. It is shown that the current amplitude can be modulated by the applied field. The details of the electric response strongly depend on the twist angles. The current exhibits periodicity for geometries where the flux through the plaquettes of the ladder can be cancelled pairwise (commensurate twist). Further twisting the geometry and changing its length causes complex aperiodic oscillations. We also study persistent currents: They reduce to simple harmonic oscillations if the system is commensurate, otherwise deviations occur due to the existence of closed paths leading to a washboard shape.Comment: 11 pages, 4 figure

A Path Integral Approach to Effective Non-Linear Medium

In this article, we propose a new method to compute the effective properties of non-linear disordered media. We use the fact that the effective constants can be defined through the minimum of an energy functional. We express this minimum in terms of a path integral allowing us to use many-body techniques. We obtain the perturbation expansion of the effective constants to second order in disorder, for any kind of non-linearity. We apply our method to both cases of strong and weak non-linearities. Our results are in agreement with previous ones, and could be easily extended to other types of non-linear problems in disordered systems.Comment: 7 page

Variational charge renormalization in charged systems

We apply general variational techniques to the problem of the counterion distribution around highly charged objects where strong condensation of counterions takes place. Within a field-theoretic formulation using a fluctuating electrostatic potential, the concept of surface-charge renormalization is recovered within a simple one-parameter variational procedure. As a test, we reproduce the Poisson-Boltzmann surface potential for a single charge planar surface both in the weak-charge and strong-charge regime. We then apply our techniques to non-planar geometries where closed-form solutions of the non-linear Poisson-Boltzmann equation are not available. In the cylindrical case, the Manning charge renormalization result is obtained in the limit of vanishing salt concentration. However, for intermediate salt concentrations a slow crossover to the non-charge-renormalized regime (at high salt) is found with a quasi-power-law behavior which helps to understand conflicting experimental and theoretical results for the electrostatic persistence length of polyelectrolytes. In the spherical geometry charge renormalization is only found at intermediate salt concentrations

Beyond Poisson-Boltzmann: Fluctuations and Correlations

We formulate the non-linear field theory for a fluctuating counter-ion distribution in the presence of a fixed, arbitrary charge distribution. The Poisson-Boltzmann equation is obtained as the saddle-point, and the effects of fluctuations and correlations are included by a loop-wise expansion around this saddle point. We show that the Poisson equation is obeyed at each order in the loop expansion and explicitly give the expansion of the Gibbs potential up to two loops. We then apply our formalism to the case of an impenetrable, charged wall, and obtain the fluctuation corrections to the electrostatic potential and counter-ion density to one-loop order without further approximations. The relative importance of fluctuation corrections is controlled by a single parameter, which is proportional to the cube of the counter-ion valency and to the surface charge density. We also calculate effective interactions between charged particles, which reflect counter-ion correlation effects.Comment: 12 pages, 8 postscript figure

Beyond Poisson-Boltzmann: Numerical sampling of charge density fluctuations

We present a method aimed at sampling charge density fluctuations in Coulomb systems. The derivation follows from a functional integral representation of the partition function in terms of charge density fluctuations. Starting from the mean-field solution given by the Poisson-Boltzmann equation, an original approach is proposed to numerically sample fluctuations around it, through the propagation of a Langevin like stochastic partial differential equation (SPDE). The diffusion tensor of the SPDE can be chosen so as to avoid the numerical complexity linked to long-range Coulomb interactions, effectively rendering the theory completely local. A finite-volume implementation of the SPDE is described, and the approach is illustrated with preliminary results on the study of a system made of two like-charge ions immersed in a bath of counter-ions

Improved RNA pseudoknots prediction and classification using a new topological invariant

We propose a new topological characterization of RNA secondary structures with pseudoknots based on two topological invariants. Starting from the classic arc-representation of RNA secondary structures, we consider a model that couples both I) the topological genus of the graph and II) the number of crossing arcs of the corresponding primitive graph. We add a term proportional to these topological invariants to the standard free energy of the RNA molecule, thus obtaining a novel free energy parametrization which takes into account the abundance of topologies of RNA pseudoknots observed in RNA databases.Comment: 9 pages, 6 figure