相关论文: Pseudoknot RNA Structures with Arc-Length $\ge 3$
We study a matrix model of RNA in which an external perturbation acts on n nucleotides of the polymer chain. The effect of the perturbation appears in the exponential generating function of the partition function as a factor…
It had been proposed that overstretching double stranded DNA from the 5-5 ends will produce a new fiber form of dsDNA that is narrower than the S form that has been suggested to result when the dsDNA is overstretched from the 3-3 ends. We…
Let $M^3 \subset \mathbb{C}^2$ be a $\mathcal{C}^\omega$ Levi nondegenerate hypersurface. In the literature, Cartan-Moser chains are detected from rather advanced considerations: either from the construction of a Cartan connection…
Arc-annotated sequences are useful for representing structural information of RNAs and have been extensively used for comparing RNA structures in both terms of sequence and structural similarities. Among the many paradigms referring to…
In this research we continue our previous investigation of wreath product normal structure \cite{SkuESL}. We generalize the group of unimodular matrices \cite{Amit} and find its structure. For this goal we propose one extension of the…
Next-generation sequencing (NGS) technologies allow new methodologies for alternative splicing (AS) analysis. Current computational methods for AS from NGS data are mainly focused on predicting splice site junctions or de novo assembly of…
In this paper we present an algorithm that generates $k$-noncrossing, $\sigma$-modular diagrams with uniform probability. A diagram is a labeled graph of degree $\le 1$ over $n$ vertices drawn in a horizontal line with arcs $(i,j)$ in the…
Non-coding RNA molecules fold into precise base pairing patterns to carry out critical roles in genetic regulation and protein synthesis. We show here that coupling systematic mutagenesis with high-throughput SHAPE chemical mapping enables…
Long length-scale structural deformations of DNA play a central role in many biological processes including gene expression. The elastic rod model, which uses a continuum approximation, has emerged as a viable tool to model deformations of…
Polycrystalline samples of the layered iron arsenides Sr2CrO3FeAs and Ba2ScO3FeAs were synthesized by high temperature solid state reactions and their crystal structures determined by the X-ray powder diffraction. Their structures are…
We show the existence of 112 non-singular rational curves on the supersingular K3 surface with Artin invariant 1 in characteristic 3 by several ways. Using these rational curves, we have a $(16)_{10}$-configuration and a $(280_{4},…
The structure function, S(k), for the s=1, Haldane gap antiferromagnetic chain, is measured accurately using the recent density matrix renormalization group method, with chain-length 100. Excellent agreement with the nonlinear $\sigma$…
Atomistic simulations were utilized to develop fundamental insights regarding the elongation process starting from ultranarrow graphene nanoribbons (GNRs) and resulting in monatomic carbon chains (MACCs). There are three key findings.…
The $k$-core percolation is a fundamental structural transition in complex networks. Through the analysis of the size jump behaviors of $k$-core in the evolution process of networks, we confirm that $k$-core percolation is continuous phase…
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.
In previous work, we gave asymptotic counting results for the number of tree-child and normal networks with $k$ reticulation vertices and explicit exponential generating functions of the counting sequences for $k=1,2,3$. The purpose of this…
Thermal decomposition of vicinal 6H-SiC(0001) surfaces with off-angles toward the $[1\bar{1}00]$ direction results in the appearance of pairs of (0001) macroterraces and $(1\bar{1}0n)$ macrofacets covered with graphene, as follows. A…
Silicon carbide (SiC) is an excellent substrate for growth and manipulation of large scale, high quality epitaxial graphene. On the carbon face (the ($\bar{1}\bar{1}\bar{1}$) or $(000\bar{1}$) face, depending on the polytype), the onset of…
Within biology, it is of interest to construct DNA complexes of a certain shape. These complexes can be represented through graph theory, using edges to model strands of DNA joined at junctions, represented by vertices. Because guided…
A family of $k$-element subsets of an $n$-element set is called 3-wise intersecting if any three members in the family have non-empty intersection. We determine the maximum size of such families exactly or asymptotically. One of our results…