Related papers: Parametric analysis of RNA folding
Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are interaction structures, that can be represented as diagrams with…
Researchers have repeatedly found that the ends of an RNA sequence are significantly closer than expected for a random linear chain. However, we prove that the ends of a branched structure are almost certainly close. Our results are…
RNA is a fundamental class of biomolecules that mediate a large variety of molecular processes within the cell. Computational algorithms can be of great help in the understanding of RNA structure-function relationship. One of the main…
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 formulate the RNA folding problem as an $N\times N$ matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
Simulated nucleotide sequences are widely used in theoretical and empirical molecular evolution studies. Conventional simulators generally use fixed parameter time-homogeneous Markov model for sequence evolution. In this work, we use the…
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…
The Nearest Neighbor model is the $\textit{de facto}$ thermodynamic model of RNA secondary structure formation and is a cornerstone of RNA structure prediction and sequence design. The current functional form (Turner 2004) contains…
This contribution focuses on the fascinating RNA molecule, its sequence-dependent folding driven by base-pairing interactions, the interplay between these interactions and natural evolution, and its multiple regulatory roles. The four of us…
A new statistical method of alignment of two heteropolymers which can form hierarchical cloverleaf-like secondary structures is proposed. This offers a new constructive algorithm for quantitative determination of binding free energy of two…
Metrics for indirectly predicting the folding rates of RNA sequences are of interest. In this letter, we introduce a simple metric of RNA structural complexity, which accounts for differences in the energetic contributions of RNA base…
We construct a minimalist model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four or six-letter alphabets. With only two…
A quantitative characterization of the relationship between molecular sequence and structure is essential to improve our understanding of how function emerges. This particular genotype-phenotype map has been often studied in the context of…
The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…
The relationship between sequences and secondary structures or shapes in RNA exhibits robust statistical properties summarized by three notions: (1) the notion of a typical shape (that among all sequences of fixed length certain shapes are…
The structure of an RNA molecule plays a significant role in its biological function. Predicting structure given a one dimensional sequence of RNA nucleotide bases is a difficult and important problem. Many computer programs (known as in…
We analyze the thermodynamic properties of a simplified model for folded RNA molecules recently studied by G. Vernizzi, H. Orland, A. Zee (in {\it Phys. Rev. Lett.} {\bf 94} (2005) 168103). The model consists of a chain of one-flavor base…
A linear external perturbation is introduced in the action of the partition function of the random matrix model of RNA [G. Vernizzi, H. Orland and A. Zee, Phys. Rev. Lett. 94, 168103 (2005)]. It is seen that (i). the perturbation…