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We enumerate possible topologies of pseudoknots in single-stranded RNA molecules. We use a steepest-descent approximation in the large N matrix field theory, and a Feynman diagram formalism to describe the resulting pseudoknot structure.

A disorder-dependent Gaussian variational approach is applied to the problem of a $d$ dimensional polymer chain in a random medium (or potential). Two classes of variational solutions are obtained. For $d<2$, these two classes may be interpreted as domain and domain wall. The critical exponent $\nu$ describing the polymer width is $\nu={1\over (4-d)}$ (domain solution) or $\nu={3\over (d+4)}$ (domain wall solution). The domain wall solution is equivalent to the (full) replica symmetry breaking variational result. For $d>2$, we find $\nu={1\over 2}$. No evidence of a phase transition is found for $2< d< 4$: one of the variational solutions suggests that the polymer chain breaks into Imry-Ma segments, whose probability distribution is calculated. For $d>4$, the other variational solution undergoes a phase transition, which has some similarity with B. Derrida's random energy models., Comment: Plain latex file

We consider a lattice model of a semiflexible homopolymer chain in a bad solvent. Beside the temperature $T$, this model is described by (i) a curvature energy $\varepsilon_h$, representing the stiffness of the chain (ii) a nearest-neighbour attractive energy $\varepsilon_v$, representing the solvent (iii) the monomer density $\rho={N \over \Omega}$, where $N$ and $\Omega$ denote respectively the number of monomers and the number of lattice sites. This model is a simplified view of the protein folding problem, which encompasses the geometrical competition between secondary structures (the curvature term modelling helix formation) and the global compactness (modeled here by the attractive energy), but contains no side chain information..., Comment: 17 pages, plain tex, 2 figures available upon request

A disorder-dependent Gaussian variational approach is applied to the $d$-dimensional ferromagnetic XY model in a random field. The randomness yields a non extensive contribution to the variational free energy, implying a random mass term in correlation functions. The Imry-Ma low temperature result, concerning the existence ($d>4$) or absence ($d < 4$) of long-range order is obtained in a transparent way. The physical picture which emerges below $d=4$ is that of a marginally stable mixture of domains. We also calculate within this variational scheme, disorder dependent correlation functions, as well as the probability distribution of the Imry-Ma domain size., Comment: 14 pages, latex file

The stability of the random field Ising model (RFIM) against spin glass (SG) fluctuations, as investigated by M\'ezard and Young, is naturally expressed via Legendre transforms, stability being then associated with the non-negativeness of eigenvalues of the inverse of a generalized SG susceptibility matrix. It is found that the signal for the occurrence of the SG transition will manifest itself in free-energy {\sl fluctuations\/} only, and not in the free energy itself. Eigenvalues of the inverse SG susceptibility matrix is then approached by the Rayleigh Ritz method which provides an upper bound. Coming from the paramagnetic phase {\sl on the Curie line,\/} one is able to use a virial-like relationship generated by scaling the {\sl single\/} unit length $ (D<6; $ in higher dimension a new length sets in, the inverse momentum cut off). Instability towards a SG phase being probed on pairs of {\sl distinct\/} replicas, it follows that, despite the repulsive coupling of the RFIM the effective pair coupling is {\sl attractive\/} (at least for small values of the parameter $ g\bar \Delta , $ $ g $ the coupling and $ \bar \Delta $ the effective random field fluctuation). As a result, \lq\lq bound states\rq\rq\ associated with replica pairs (negative eigenvalues) provide the instability signature. {\sl Away from the Curie line\/}, the attraction is damped out till the SG transition line is reached and paramagnetism restored. In $ D<6, $ the SG transition always precedes the ferromagnetic one, thus the domain in dimension where standard dimensional reduction would apply (on the Curie line) shrinks to zero., Comment: tex

We study the adsorption of polymer chains on a fluctuating surface. Physical examples are provided by polymer adsorption at the rough interface between two non-miscible liquids, or on a membrane. In a mean-field approach, we find that the self--avoiding chains undergo an adsorption transition, accompanied by a stiffening of the fluctuating surface. In particular, adsorption of polymers on a membrane induces a surface tension and leads to a strong suppression of roughness., Comment: REVTEX, 9 pages, no figures

We study a single statistical amphiphilic copolymer chain AB in a selective solvent (e.g.water). Two situations are considered. In the annealed case, hydrophilic (A) and hydrophobic (B) monomers are at local chemical equilibrium and both the fraction of A monomers and their location along the chain can vary, whereas in the quenched case (which is relevant to proteins), the chemical sequence along the chain is fixed by synthesis. In both cases, the physical behaviour depends on the average hydrophobicity of the polymer chain. For a strongly hydrophobic chain (large fraction of B), we find an ordinary continuous $\theta$ collapse, with a large conformational entropy in the collapsed phase. For a weakly hydrophobic, or a hydrophilic chain, there is an unusual first-order collapse transition. In particular, for the case of Gaussian disorder, this discontinuous transition is driven by a change of sign of the third virial coefficient. The entropy of this collapsed phase is strongly reduced with respect to the $\theta$ collapsed phase. Email contact: orland@amoco.saclay.cea.fr, Comment: Saclay-T94/077 Email: orland@amoco.saclay.cea.fr

The Flory theory for a single polymer chain is derived as the lowest order of a cumulant expansion. In this approach, the full original Flory free energy (including the logarithmic term), is recovered. %This term does not change the wandering exponent $ \nu $ but turns out to %be responsible for the crossover from Brownian $ (d>4) $ to swollen $ %(d\leq4) $ %regime. The prefactors of the elastic and repulsive energy are calculated from the microscopic parameters. The method can be applied to other types of monomer-monomer interactions, and the case of a single chain in a bad solvent is discussed . The method is easily generalized to many chain systems (polymers in solutions), yielding the usual crossovers with chain concentration. Finally, this method is suitable for a systematic expansion around the Flory theory. The corrections to Flory theory consist of extensive terms (proportional to the number $N$ of monomers) and powers of $N^{2-\nu d}$ . These last terms diverge in the thermodynamic limit, but less rapidly than the usual Fixman expansion in $N^{2- d/2}$., Comment: Email contact: orland@amoco.saclay.cea.fr

We study local energy minima of twenty(L-alanine). The minima are generated using high-temperature Molecular Dynamics and Chain-Growth Monte Carlo simulations, with subsequent minimization. We find that the lower-energy configurations are $ \alpha $-helices for a wide range of dielectric constant values $ (\epsilon = 1,10,80), $ and that there is no noticeable difference between the distribution of energy minima in $ \phi \psi $ space for different values of $ \epsilon . $ Ultrametricity tests show that lower-energy $ (\alpha $ -helical) $ \epsilon =1 $ configurations form a set which is ultrametric to a certain degree, providing evidence for the presence of fine structure among those minima. We put forward a heuristic argument for this fine structure. We also find evidence for ultrametricity of a different kind among $ \epsilon =10 $ and $ \epsilon =80 $ energy minima. We analyze the distribution of lengths of $ \alpha $-helical portions among the minimized configurations and find a persistence phenomenon for the $ \epsilon =1 $ ones, in qualitative agreement with previous studies of critical lengths. Email contact: bascle@amoco.saclay.cea.fr, Comment: Saclay-T93/025 Email: bascle@amoco.saclay.cea.fr