Statistical Physics of RNA-folding

We discuss the physics of RNA as described by its secondary structure. We examine the static properties of a homogeneous RNA-model that includes pairing and base stacking energies as well as entropic costs for internal loops. For large enough costs the model exhibits a thermal denaturation transition which we analyze in terms of the radius of gyration. We point out an inconsistency in the standard approach to RNA secondary structure prediction for large molecules. Under an external force a second order phase transition between a globular and an extended phase takes place. A Harris-type criterion shows that sequence disorder does not affect the correlation length exponent while the other critical exponents are modified in the glass phase. However, at high temperatures, on a coarse-grained level, disordered RNA is well described by a homogeneous model. The characteristics of force-extension curves are discussed as a function of the energy parameters. We show that the force transition is always second order. A re-entrance phenomenon relevant for real disordered RNA is predicted.Comment: accepted for publication in Phys. Rev.

Reversibility of Arctic Sea Ice Retreat - A Multi-Scale Modeling Approach

Arctic summer sea ice has been retreating rapidly over past decade. Climate model projections show further retreat under typical forcing scenarios. The mode of the retreat is a matter of debate. Low-order models show reversible and irreversible retreat depending on the shape of the albedo parametrization. Climate models do not show irreversible sea ice losses, but generally underestimate the current trend of retreat

Monte Carlo simulations of interfaces in polymer blends

We review recent simulation studies of interfaces between immiscible homopolymer phases. Special emphasis is given to the presentation of efficient simulation techniques and powerful methods of data analysis, such as the analysis of capillary wave spectra. Possible reasons for polymer incompatibility and ways to relate model dependent interaction parameters to an effective Flory Huggins parameter are discussed. Various interfaces are then considered and characterised with respect to their microscopic structure and thermodynamic properties. In particular, interfaces between homopolymers of equal or disparate stiffness are studied, interfaces containing diblock copolymers, and interfaces confined in thin films. The results are related to the phase behaviour of ternary homopolymer/copolymer systems, and to wetting transitions in thin films.Comment: To appear in Annual Reviews of Computational Physics, edt. D. Stauffe

Wetting and Capillary Condensation in Symmetric Polymer Blends: A comparison between Monte Carlo Simulations and Self-Consistent Field Calculations

We present a quantitative comparison between extensive Monte Carlo simulations and self-consistent field calculations on the phase diagram and wetting behavior of a symmetric, binary (AB) polymer blend confined into a film. The flat walls attract one component via a short range interaction. The critical point of the confined blend is shifted to lower temperatures and higher concentrations of the component with the lower surface free energy. The binodals close the the critical point are flattened compared to the bulk and exhibit a convex curvature at intermediate temperatures -- a signature of the wetting transition in the semi-infinite system. Investigating the spectrum of capillary fluctuation of the interface bound to the wall, we find evidence for a position dependence of the interfacial tension. This goes along with a distortion of the interfacial profile from its bulk shape. Using an extended ensemble in which the monomer-wall interaction is a stochastic variable, we accurately measure the difference between the surface energies of the components, and determine the location of the wetting transition via the Young equation. The Flory-Huggins parameter at which the strong first order wetting transition occurs is independent of chain length and grows quadratically with the integrated wall-monomer interaction strength. We estimate the location of the prewetting line. The prewetting manifests itself in a triple point in the phase diagram of very thick films and causes spinodal dewetting of ultrathin layers slightly above the wetting transition. We investigate the early stage of dewetting via dynamic Monte Carlo simulations.Comment: to appear in Macromolecule

The secondary structure of RNA under tension

We study the force-induced unfolding of random disordered RNA or single-stranded DNA polymers. The system undergoes a second order phase transition from a collapsed globular phase at low forces to an extensive necklace phase with a macroscopic end-to-end distance at high forces. At low temperatures, the sequence inhomogeneities modify the critical behaviour. We provide numerical evidence for the universality of the critical exponents which, by extrapolation of the scaling laws to zero force, contain useful information on the ground state (f=0) properties. This provides a good method for quantitative studies of scaling exponents characterizing the collapsed globule. In order to get rid of the blurring effect of thermal fluctuations we restrict ourselves to the groundstate at fixed external force. We analyze the statistics of rearrangements, in particular below the critical force, and point out its implications for force-extension experiments on single molecules.Comment: to be published in Europhys. J.

Combined Interpolation Scheme for Transition and Noble Metals

Combined interpolation scheme for calculating energy bands of transition and noble metal