相关论文: The secondary structure of RNA under tension
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…
Loops are essential secondary structure elements in folded DNA and RNA molecules and proliferate close to the melting transition. Using a theory for nucleic acid secondary structures that accounts for the logarithmic entropy c ln m for a…
We describe quantitatively a RNA molecule under the influence of an external force exerted at its two ends as in a typical single-molecule experiment. Our calculation incorporates the interactions between nucleotides by using the…
We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force…
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…
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…
A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for…
We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA (dsDNA). When the pulling force is increased to a critical value, an ``unzipping'' transition occurs. For random…
The Laessig-Wiese (LW) field theory for the freezing transition of random RNA secondary structures is generalized to the situation of an external force. We find a second-order phase transition at a critical applied force f = f_c. For f <…
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…
RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by…
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…
Formation of base pairs between the nucleotides of an RNA sequence gives rise to a complex and often highly branched RNA structure. While numerous studies have demonstrated the functional importance of the high degree of RNA branching --…
When pulled along the axis, double-strand DNA undergoes a large conformational change and elongates roughly twice its initial contour length at a pulling force about 70 pN. The transition to this highly overstretched form of DNA is very…
We study the effect of random forces on a double stranded DNA in unzipping the two strands, analogous to the problem of an adsorbed polymer under a random force. The ground state develops bubbles of various lengths as the random force…
We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…
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 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…
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 summarize the recent simulation progress of micromanipulation experiments on RNAs. Our work mainly consults with two important small RNAs unfolding experiments carried out by Bustamante group. Our results show that, in contrast to…