Force-induced misfolding in RNA

RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of its importance in modern biophysics, the current understanding of RNA folding kinetics is limited by the complex interplay between the weak base-pair interactions that stabilize the native structure and the disordering effect of thermal forces. The possibility of mechanically pulling individual molecules offers a new perspective to understand the folding of nucleic acids. Here we investigate the folding and misfolding mechanism in RNA secondary structures pulled by mechanical forces. We introduce a model based on the identification of the minimal set of structures that reproduce the patterns of force-extension curves obtained in single molecule experiments. The model requires only two fitting parameters: the attempt frequency at the level of individual base pairs and a parameter associated to a free energy correction that accounts for the configurational entropy of an exponentially large number of neglected secondary structures. We apply the model to interpret results recently obtained in pulling experiments in the three-helix junction S15 RNA molecule (RNAS15). We show that RNAS15 undergoes force-induced misfolding where force favors the formation of a stable non-native hairpin. The model reproduces the pattern of unfolding and refolding force-extension curves, the distribution of breakage forces and the misfolding probability obtained in the experiments.Comment: 28 pages, 11 figure

Grand canonical and canonical solution of self-avoiding walks with up to three monomers per site on the Bethe lattice

We solve a model of polymers represented by self-avoiding walks on a lattice which may visit the same site up to three times in the grand-canonical formalism on the Bethe lattice. This may be a model for the collapse transition of polymers where only interactions between monomers at the same site are considered. The phase diagram of the model is very rich, displaying coexistence and critical surfaces, critical, critical endpoint and tricritical lines, as well as a multicritical point. From the grand-canonical results, we present an argument to obtain the properties of the model in the canonical ensemble, and compare our results with simulations in the literature. We do actually find extended and collapsed phases, but the transition between them, composed by a line of critical endpoints and a line of tricritical points, separated by the multicritical point, is always continuous. This result is at variance with the simulations for the model, which suggest that part of the line should be a discontinuous transition. Finally, we discuss the connection of the present model with the standard model for the collapse of polymers (self-avoiding self-attracting walks), where the transition between the extended and collapsed phases is a tricritical point.Comment: 34 pages, including 10 figure

Surface critical behaviour of the Interacting Self-Avoiding Trail on the square lattice

The surface critical behaviour of the interacting self-avoiding trail is examined using transfer matrix methods coupled with finite-size scaling. Particular attention is paid to the critical exponents at the ordinary and special points along the collapse transition line. The phase diagram is also presented.Comment: Journal of Physics A (accepted

Diffusive transport of light in three-dimensional disordered Voronoi structures

The origin of diffusive transport of light in dry foams is still under debate. In this paper, we consider the random walks of photons as they are reflected or transmitted by liquid films according to the rules of ray optics. The foams are approximately modeled by three-dimensional Voronoi tessellations with varying degree of disorder. We study two cases: a constant intensity reflectance and the reflectance of thin films. Especially in the second case, we find that in the experimentally important regime for the film thicknesses, the transport-mean-free path does not significantly depend on the topological and geometrical disorder of the Voronoi foams including the periodic Kelvin foam. This may indicate that the detailed structure of foams is not crucial for understanding the diffusive transport of light. Furthermore, our theoretical values for transport-mean-free path fall in the same range as the experimental values observed in dry foams. One can therefore argue that liquid films contribute substantially to the diffusive transport of light in {dry} foams.Comment: 8 pages, 8 figure

Diffusive transport of light in two-dimensional granular materials

We study photon diffusion in a two-dimensional random packing of monodisperse disks as a simple model of granular material. We apply ray optics approximation to set up a persistent random walk for the photons. We employ Fresnel's intensity reflectance with its rich dependence on the incidence angle and polarization state of the light. We present an analytic expression for the transport-mean-free path in terms of the refractive indices of grains and host medium, grain radius, and packing fraction. We perform numerical simulations to examine our analytical result.Comment: 9 pages, 3 figure

Polymer Brushes in Cylindrical Pores: Simulation versus Scaling Theory

The structure of flexible polymers endgrafted in cylindrical pores of diameter D is studied as a function of chain length N and grafting density \sigma, assuming good solvent conditions. A phenomenological scaling theory, describing the variation of the linear dimensions of the chains with \sigma, is developed and tested by Molecular Dynamics simulations of a bead-spring model.Comment: 35 pages, 38 figure

Distance dependence of angular correlations in dense polymer solutions

Angular correlations in dense solutions and melts of flexible polymer chains are investigated with respect to the distance $r$ between the bonds by comparing quantitative predictions of perturbation calculations with numerical data obtained by Monte Carlo simulation of the bond-fluctuation model. We consider both monodisperse systems and grand-canonical (Flory-distributed) equilibrium polymers. Density effects are discussed as well as finite chain length corrections. The intrachain bond-bond correlation function $P(r)$ is shown to decay as $P(r) \sim 1/r^3$ for \xi \ll r \ll \r^* with $\xi$ being the screening length of the density fluctuations and $r^* \sim N^{1/3}$ a novel length scale increasing slowly with (mean) chain length $N$.Comment: 17 pages, 5 figures, accepted for publication at Macromolecule

Critical Indices as Limits of Control Functions

A variant of self-similar approximation theory is suggested, permitting an easy and accurate summation of divergent series consisting of only a few terms. The method is based on a power-law algebraic transformation, whose powers play the role of control functions governing the fastest convergence of the renormalized series. A striking relation between the theory of critical phenomena and optimal control theory is discovered: The critical indices are found to be directly related to limits of control functions at critical points. The method is applied to calculating the critical indices for several difficult problems. The results are in very good agreement with accurate numerical data.Comment: 1 file, 5 pages, RevTe

Critical Dynamics of Gelation

Shear relaxation and dynamic density fluctuations are studied within a Rouse model, generalized to include the effects of permanent random crosslinks. We derive an exact correspondence between the static shear viscosity and the resistance of a random resistor network. This relation allows us to compute the static shear viscosity exactly for uncorrelated crosslinks. For more general percolation models, which are amenable to a scaling description, it yields the scaling relation $k=\phi-\beta$ for the critical exponent of the shear viscosity. Here $\beta$ is the thermal exponent for the gel fraction and $\phi$ is the crossover exponent of the resistor network. The results on the shear viscosity are also used in deriving upper and lower bounds on the incoherent scattering function in the long-time limit, thereby corroborating previous results.Comment: 34 pages, 2 figures (revtex, amssymb); revised version (minor changes

Critical behavior of a one-dimensional monomer-dimer reaction model with lateral interactions

A monomer-dimer reaction lattice model with lateral repulsion among the same species is studied using a mean-field analysis and Monte Carlo simulations. For weak repulsions, the model exhibits a first-order irreversible phase transition between two absorbing states saturated by each different species. Increasing the repulsion, a reactive stationary state appears in addition to the saturated states. The irreversible phase transitions from the reactive phase to any of the saturated states are continuous and belong to the directed percolation universality class. However, a different critical behavior is found at the point where the directed percolation phase boundaries meet. The values of the critical exponents calculated at the bicritical point are in good agreement with the exponents corresponding to the parity-conserving universality class. Since the adsorption-reaction processes does not lead to a non-trivial local parity-conserving dynamics, this result confirms that the twofold symmetry between absorbing states plays a relevant role in determining the universality class. The value of the exponent $\delta_2$, which characterizes the fluctuations of an interface at the bicritical point, supports the Bassler-Brown's conjecture which states that this is a new exponent in the parity-conserving universality class.Comment: 19 pages, 22 figures, to be published in Phys. Rev