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On the Coloring of Pseudoknots  [PDF]
Allison Henrich,Slavik Jablan
Mathematics , 2013,
Abstract: Pseudodiagrams are diagrams of knots where some information about which strand goes over/under at certain crossings may be missing. Pseudoknots are equivalence classes of pseudodiagrams, with equivalence defined by a class of Reidemeister-type moves. In this paper, we introduce two natural extensions of classical knot colorability to this broader class of knot-like objects. We use these definitions to define the determinant of a pseudoknot (i.e. the pseudodeterminant) that agrees with the classical determinant for classical knots. Moreover, we extend Conway notation to pseudoknots to facilitate the investigation of families of pseudoknots and links. The general formulae for pseudodeterminants of pseudoknot families may then be used as a criterion for p-colorability of pseudoknots.
The Theory of Pseudoknots  [PDF]
Allison Henrich,Rebecca Hoberg,Slavik Jablan,Lee Johnson,Elizabeth Minten,Ljiljana Radovic
Mathematics , 2012, DOI: 10.1142/S0218216513500326
Abstract: Classical knots in $\mathbb{R}^3$ can be represented by diagrams in the plane. These diagrams are formed by curves with a finite number of transverse crossings, where each crossing is decorated to indicate which strand of the knot passes over at that point. A pseudodiagram is a knot diagram that may be missing crossing information at some of its crossings. At these crossings, it is undetermined which strand passes over. Pseudodiagrams were first introduced by Ryo Hanaki in 2010. Here, we introduce the notion of a pseudoknot, i.e. an equivalence class of pseudodiagrams under an appropriate choice of Reidemeister moves. In order to begin a classification of pseudoknots, we introduce the concept of a weighted resolution set, an invariant of pseudoknots. We compute the weighted resolution set for several pseudoknot families and discuss notions of crossing number, homotopy, and chirality for pseudoknots.
Prediction for RNA planar pseudoknots
Li Hengwu,Zhu Daming,Liu Zhendong,Li Hong,
Li Hengwu
,Zhu Daming,Liu Zhendong and Li Hong

自然科学进展 , 2007,
Abstract: Based on m-stems and semi-extensible structure, a model is presented to represent RNA planar pseudoknots, and corresponding dynamic programming algorithm is designed and implemented to predict arbitrary planar pseudoknots and simple non-planar pseudoknots with O(n4) time and O(n3) space. The algorithm folds total 245 sequences in the Pseudobase database, and the test results indicate that the algorithm has good accuracy, sensitivity and specificity.
International Journal of Bioinformatics Research , 2011,
Abstract: Snurps or small nuclear ribonucleoproteins (snRNPs), are RNA-protein complexes that combine withunmodified pre-mRNA and various other proteins to form a Spliceosome, comprising of five small nuclear RNAs(snRNAs)—U1, U2, U4, U5, and U6 snRNA—as well as many protein factors, upon which splicing of pre-mRNAoccurs. While, RNA pseudoknots play crucial role in protein synthesis by helping in internal ribosome entry,frameshifting, stop codon readthrough in many viral species and the 3’NCR pseudoknots helps viral RNAs to replicate,has been reported by a number of investigators, its presence in human snurps has not yet been done. The present insilico study reveals the presence of pseudoknots in the mRNAs of the proteins associated with human Spliceosome. Itnot only emphasizes their significance as catalytic RNA world relics but also opens the scope of research in thefunctional and structural associations of RNA pseudoknots in eukaryotic gene regulation.
Isotopy and Homotopy Invariants of Classical and Virtual Pseudoknots  [PDF]
Francois Dorais,Allison Henrich,Slavik Jablan,Inga Johnson
Mathematics , 2013,
Abstract: Pseudodiagrams are knot or link diagrams where some of the crossing information is missing. Pseudoknots are equivalence classes of pseudodiagrams, where equivalence is generated by a natural set of Reidemeister moves. In this paper, we introduce a Gauss-diagrammatic theory for pseudoknots which gives rise to the notion of a virtual pseudoknot. We provide new, easily computable isotopy and homotopy invariants for classical and virtual pseudodiagrams. We also give tables of unknotting numbers for homotopically trivial pseudoknots and homotopy classes of homotopically nontrivial pseudoknots. Since pseudoknots are closely related to singular knots, this work also has implications for the classification of classical and virtual singular knots.
Prediction of RNA pseudoknots by Monte Carlo simulations  [PDF]
G. Vernizzi,H. Orland,A. Zee
Quantitative Biology , 2004,
Abstract: In this paper we consider the problem of RNA folding with pseudoknots. We use a graphical representation in which the secondary structures are described by planar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze the non-planar topologies of RNA structures and propose a classification of RNA pseudoknots according to the minimal genus of the surface on which the RNA structure can be embedded. This classification provides a simple and natural way to tackle the problem of RNA folding prediction in presence of pseudoknots. Based on that approach, we describe a Monte Carlo algorithm for the prediction of pseudoknots in an RNA molecule.
Combinatorics Of RNA Structures With Pseudoknots  [PDF]
Emma Y. Jin,Jing Qin,Christian M. Reidys
Mathematics , 2007,
Abstract: In this paper we derive the generating function of RNA structures with pseudoknots. We enumerate all $k$-noncrossing RNA pseudoknot structures categorized by their maximal sets of mutually intersecting arcs. In addition we enumerate pseudoknot structures over circular RNA. For 3-noncrossing RNA structures and RNA secondary structures we present a novel 4-term recursion formula and a 2-term recursion, respectively. Furthermore we enumerate for arbitrary $k$ all $k$-noncrossing, restricted RNA structures i.e. $k$-noncrossing RNA structures without 2-arcs i.e. arcs of the form $(i,i+2)$, for $1\le i\le n-2$.
A steepest descent calculation of RNA pseudoknots  [PDF]
M. Pillsbury,H. Orland,A. Zee
Physics , 2002, DOI: 10.1103/PhysRevE.72.011911
Abstract: We enumerate possible topologies of pseudoknots in single-stranded RNA molecules. We use a steepest-descent approximation in the large N matrix field theory, and a Feynman diagram formalism to describe the resulting pseudoknot structure.
Asymptotic Enumeration of RNA Structures with Pseudoknots  [PDF]
Emma Y. Jin,Christian M. Reidys
Quantitative Biology , 2007,
Abstract: In this paper we present the asymptotic enumeration of RNA structures with pseudoknots. We develop a general framework for the computation of exponential growth rate and the sub exponential factors for $k$-noncrossing RNA structures. Our results are based on the generating function for the number of $k$-noncrossing RNA pseudoknot structures, ${\sf S}_k(n)$, derived in \cite{Reidys:07pseu}, where $k-1$ denotes the maximal size of sets of mutually intersecting bonds. We prove a functional equation for the generating function $\sum_{n\ge 0}{\sf S}_k(n)z^n$ and obtain for $k=2$ and $k=3$ the analytic continuation and singular expansions, respectively. It is implicit in our results that for arbitrary $k$ singular expansions exist and via transfer theorems of analytic combinatorics we obtain asymptotic expression for the coefficients. We explicitly derive the asymptotic expressions for 2- and 3-noncrossing RNA structures. Our main result is the derivation of the formula ${\sf S}_3(n) \sim \frac{10.4724\cdot 4!}{n(n-1)...(n-4)} (\frac{5+\sqrt{21}}{2})^n$.
Early Stages of Homopolymer Collapse  [PDF]
A. Halperin,Paul M. Goldbart
Physics , 1999, DOI: 10.1103/PhysRevE.61.565
Abstract: Interest in the protein folding problem has motivated a wide range of theoretical and experimental studies of the kinetics of the collapse of flexible homopolymers. In this Paper a phenomenological model is proposed for the kinetics of the early stages of homopolymer collapse following a quench from temperatures above to below the theta temperature. In the first stage, nascent droplets of the dense phase are formed, with little effect on the configurations of the bridges that join them. The droplets then grow by accreting monomers from the bridges, thus causing the bridges to stretch. During these two stages the overall dimensions of the chain decrease only weakly. Further growth of the droplets is accomplished by the shortening of the bridges, which causes the shrinking of the overall dimensions of the chain. The characteristic times of the three stages respectively scale as the zeroth, 1/5 and 6/5 power of the the degree of polymerization of the chain.
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