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Register a new userRNA denaturation: excluded volume, pseudoknots and transition scenarios
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A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous transition. Otherwise a smooth crossover occurs from the swollen linear polymer behavior to highly ramified, almost compact conformations with secondary structures. In the latter scenario, which is appropriate when these structures are much more stable than pseudoknot links, probability distributions for the lengths of both loops and main branches obey scaling with nonclassical exponents.
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The adsorption of charged colloids (macroions) onto an oppositely charged planar substrate is investigated theoretically. Taking properly into account the finite size of the macroions, unusual behaviors are reported. It is found that the role of the coions (the little salt-ions carrying the same sign of charge as that of the substrate) is crucial to understand the mechanisms involved in the process of macroion adsorption. In particular, the coions can accumulate near the substrates surface and lead to a counter-intuitive {it surface charge amplification}.
In this paper we consider the problem of RNA folding with pseudoknots. We use a graphical representation in which the secondary structures are described by planar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze the non-planar topologies of RNA structures and propose a classification of RNA pseudoknots according to the minimal genus of the surface on which the RNA structure can be embedded. This classification provides a simple and natural way to tackle the problem of RNA folding prediction in presence of pseudoknots. Based on that approach, we describe a Monte Carlo algorithm for the prediction of pseudoknots in an RNA molecule.
The effect of excluded volume interactions on the structure of a polymer in shear flow is investigated by Brownian Dynamics simulations for chains with size $30leq Nleq 300$. The main results concern the structure factor $S({bf q})$ of chains of N=300 Kuhn segments, observed at a reduced shear rate $beta=dot{gamma}tau=3.2$, where $dot{gamma}$ is the bare shear rate and $tau$ is the longest relaxation time of the chain. At low q, where anisotropic global deformation is probed, the chain form factor is shown to match the form factor of the continuous Rouse model under shear at the same reduced shear rate, computed here for the first time in a wide range of wave vectors. At high q, the chain structure factor evolves towards the isotropic equilibrium power law $q^{-1/ u}$ typical of self-avoiding walk statistics. The matching between excluded volume and ideal chains at small q, and the excluded volume power law behavior at large q are observed for ${bf q}$ orthogonal to the main elongation axis but not yet for ${bf q}$ along the elongation direction itself, as a result of interferences with finite extensibility effects. Our simulations support the existence of anisotropic shear blobs for polymers in good solvent under shear flow for $beta>1$ provided chains are sufficiently long.
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.
The classical bond-fluctuation model (BFM) is an efficient lattice Monte Carlo algorithm for coarse-grained polymer chains where each monomer occupies exclusively a certain number of lattice sites. In this paper we propose a generalization of the BFM where we relax this constraint and allow the overlap of monomers subject to a finite energy penalty $overlap$. This is done to vary systematically the dimensionless compressibility $g$ of the solution in order to investigate the influence of density fluctuations in dense polymer melts on various s tatic properties at constant overall monomer density. The compressibility is obtained directly from the low-wavevector limit of the static structure fa ctor. We consider, e.g., the intrachain bond-bond correlation function, $P(s)$, of two bonds separated by $s$ monomers along the chain. It is shown that the excluded volume interactions are never fully screened for very long chains. If distances smaller than the thermal blob size are probed ($s ll g$) the chains are swollen acc ording to the classical Fixman expansion where, e.g., $P(s) sim g^{-1}s^{-1/2}$. More importantly, the polymers behave on larger distances ($s gg g$) like swollen chains of incompressible blobs with $P(s) si m g^0s^{-3/2}$.
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