Related papers: Zero Temperature Properties of RNA Secondary Struc…
We characterize the low temperature phase of a simple model for RNA secondary structures by determining the typical energy scale E(l) of excitations involving l bases. At zero temperature, we find a scaling law E(l) \sim l^\theta with…
Models for RNA secondary structures (the topology of folded RNA) without pseudo knots are disordered systems with a complex state-space below a critical temperature. Hence, a complex dynamical (glassy) behavior can be expected, when…
The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models are introduced to allow detailed analytical and numerical…
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…
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…
We numerically study a disordered model for the RNA secondary structure and we find that it undergoes a phase transition, with a breaking of the replica symmetry in the low temperature region (like in spin glasses). Our results are based on…
We study the folding of RNA secondary structures with quenched sequence randomness by means of the constrained annealing method. A thermodynamic phase transition is induced by including the conformational weight of loop structures. In…
RNA forms elaborate secondary structures through intramolecular base pairing. These structures perform critical biological functions within each cell. Due to the availability of a polynomial algorithm to calculate the partition function…
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…
We analyze zero-temperature universal properties of the simplest Galilean-invariant model of spinless low-dimensional fermions with short-range two-body interactions. In particular, it is shown that after proper renormalization of the…
RNA molecules form a sequence-specific self-pairing pattern at low temperatures. We analyze this problem using a random pairing energy model as well as a random sequence model that includes a base stacking energy in favor of helix…
We study the glassy super-rough phase of a class of solid-on-solid models with a disordered substrate in the limit of vanishing temperature by means of exact ground states, which we determine with a newly developed minimum cost flow…
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…
Highly frustrated lattices yield a completely flat lowest single-electron band. Remarkably, exact many-body ground states can be constructed for the repulsive Hubbard model and the t-J model by filling this flat band with localized electron…
Folding of RNA is subject to a competition between entropy, relevant at high temperatures, and the random, or random looking, sequence, determining the low- temperature phase. It is known from numerical simulations that for random as well…
We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate…
We study secondary structures of random RNA molecules by means of a renormalized field theory based on an expansion in the sequence disorder. We show that there is a continuous phase transition from a molten phase at higher temperatures to…
Ground-state properties of a hybrid double-tetrahedral chain, in which the localized Ising spins regularly alternate with triangular plaquettes occupied by a variable number of mobile electrons, are exactly investigated. We demonstrate that…
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…
Formation of RNA secondary structures is an example of the sequence-structure problem omnipresent in biopolymers. A theoretical question of recent interest is whether a random RNA sequence undergoes a finite temperature glass transition. We…