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In this paper we enumerate $k$-noncrossing RNA pseudoknot structures with given minimum arc- and stack-length. That is, we study the numbers of RNA pseudoknot structures with arc-length $ge 3$, stack-length $ge sigma$ and in which there are at most $k-1$ mutually crossing bonds, denoted by ${sf T}_{k,sigma}^{[3]}(n)$. In particular we prove that the numbers of 3, 4 and 5-noncrossing RNA structures with arc-length $ge 3$ and stack-length $ge 2$ satisfy ${sf T}_{3,2}^{[3]}(n)^{}sim K_3 n^{-5} 2.5723^n$, ${sf T}^{[3]}_{4,2}(n)sim K_4 n^{-{21/2}} 3.0306^n$, and ${sf T}^{[3]}_{5,2}(n)sim K_5 n^{-18} 3.4092^n$, respectively, where $K_3,K_4,K_5$ are constants. Our results are of importance for prediction algorithms for RNA pseudoknot structures.
In this paper we study $k$-noncrossing RNA structures with minimum arc-length 4 and at most $k-1$ mutually crossing bonds. Let ${sf T}_{k}^{[4]}(n)$ denote the number of $k$-noncrossing RNA structures with arc-length $ge 4$ over $n$ vertices. We prov
In this paper we present a selfcontained analysis and description of the novel {it ab initio} folding algorithm {sf cross}, which generates the minimum free energy (mfe), 3-noncrossing, $sigma$-canonical RNA structure. Here an RNA structure is 3-nonc
We present a novel topological classification of RNA secondary structures with pseudoknots. It is based on the topological genus of the circular diagram associated to the RNA base-pair structure. The genus is a positive integer number, whose value qu
We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for the simple
Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex biological structur