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

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.

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

Project Bundling, Liquidity Spillovers, and Capital Market Discipline

This paper develops a theory of integration based on the inability of parties to write comprehensive financial contracts. In our model, integration comes with both benefits and costs. On the one hand, integration entails liquidity spillovers from high- to low-return projects, implying that integrated firms have better access to external finance than non-integrated firms. On the other hand, integration leads to the creation of a larger internal capital market, thereby making integrated firms less dependent on the provision of follow-up financing by outside investors. But in a world where financial contracting is incomplete, the threat not to provide follow-up financing may be the only means that investors have to make borrowers repay their debt. By making this threat less effective, integration may aggravate existing financing constraints caused by contractual incompleteness.

Cluster expansion for dimerized spin systems

We have studied dimerized spin systems by realizing the cluster expansion to high order. We have extended our previous dimer expansion for one-dimensional systems to cover weakly interacting chains for a quantitative description of three dimensional materials like PHCC and KCuCl_3. By comparison with recent inelastic neutron scattering data we are able to determine the exchange energies between individual spins. We have further investigated the incommensurate region of zigzag chains with isotropic exchange coupling constants near the disorder-line where the dispersion curve exhibits a minimum at a finite wavevector. Our approach clearly shows the gradual transition between the minimum of the dispersion at wavevector 0 and wavevector Pi within this region. The extent of the incommensurate regime is given analytically in an expansion in the coupling constants.Comment: 3 pages, 3 figures; contribution to ICNS2001; uses svjour.clo, svglobal.clo (included