Related papers: Random RNA under tension
We analyze a microscopic RNA model, which includes two widely used models as limiting cases, namely it contains terms for bond as well as for stacking energies. We numerically investigate possible changes in the qualitative and quantitative…
RNA's diversity of structures and functions impacts all life forms since primordia. We use calorimetric force spectroscopy to investigate RNA folding landscapes in previously unexplored low-temperature conditions. We find that Watson-Crick…
We examine the behavior of a model which describes the melting of double-stranded DNA chains. The model, with displacement-dependent stiffness constants and a Morse on-site potential, is analyzed numerically; depending on the stiffness…
We consider the Farey fraction spin chain in an external field $h$. Using ideas from dynamical systems and functional analysis, we show that the free energy $f$ in the vicinity of the second-order phase transition is given, exactly, by $$ f…
The effects of locally random magnetic fields are considered in a nonequilibrium Ising model defined on a square lattice with nearest-neighbors interactions. In order to generate the random magnetic fields, we have considered random…
A version of the second order phase transition theory, in which the Nernst theorem holds automatically, is proposed. The theory is constructed in terms of the order parameter and the (configurational) entropy. It faithfully reproduces the…
Monte Carlo simulations have been used to study a discretized Heisenberg ferromagnet (FM) in a random field on simple cubic lattices. The spin variable on each site is chosen from the twelve [110] directions. The random field has infinite…
Using coarse-grained model we have explored forced-unfolding of RNA hairpin as a function of $f_S$ and the loading rate ($r_f$). The simulations and theoretical analysis have been done without and with the handles that are explicitly…
We study biased random walkers on lattices with randomly dispersed static traps in one, two and three dimensions. As the external bias is increased from zero the system undergoes a phase transition, most clearly manifested in the asymptotic…
We study the effective behavior of random, heterogeneous, anisotropic, second order phase transitions energies that arise in the study of pattern formations in physical-chemical systems. Specifically, we study the asymptotic behavior, as…
We study the possibility to apply phenomenological approach to the description of magnetic transitions in UGe2 with the help of Landau free energy expanded to 8-th order in magnetisation. The analysis shows that for certain values of…
We investigate phase transitions in scalar field theories using the functional renormalization group (RG) equation. We analyze a system with $U(2)\times U(2)$ symmetry, in which there is a parameter $\lambda_2$ that controls the strength of…
A chain of singly-charged particles, confined by a harmonic potential, exhibits a sudden transition to a zigzag configuration when the radial potential reaches a critical value, depending on the particle number. This structural change is a…
In cond-mat/9907125 the low-temperature behavior of a model for RNA secondary structure was studied. It is claimed that the model exhibits a breaking of the replica symmetry, since the width of the distribution P(q) of overlaps may converge…
The influence of a local anisotropy of random orientation on a ferromagnetic phase transition is studied for two cases of anisotropy axis distribution. To this end a model of a random anisotropy magnet is analyzed by means of the field…
A brief survey of the theoretical, numerical and experimental studies of the random field Ising model during last three decades is given. Nature of the phase transition in the three-dimensional RFIM with Gaussian random fields is discussed.…
We apply Kramers theory to investigate the dissociation of multiple bonds under mechanical force and interpret experimental results for the unfolding/refolding force distributions of an RNA hairpin pulled at different loading rates using…
Mechanical unfolding of RNA structures, ranging from hairpins to ribozymes, using laser optical tweezer (LOT) experiments have begun to reveal the features of the energy landscape that cannot be easily explored using conventional…
We study first- and second-order phase transitions of ferromagnetic lattice models on scale-free networks, with a degree exponent $\gamma$. Using the example of the $q$-state Potts model we derive a general self-consistency relation within…
In this paper we study the effect of energy parameters on minimum free energy (mfe) RNA secondary structures. Employing a simplified combinatorial energy model, that is only dependent on the diagram representation and that is not sequence…