Related papers: The block spectrum of RNA pseudoknot structures
We study the amount of reliable information that can be stored in a DNA-based storage system with noisy sequencing, where each codeword is composed of short DNA molecules. We analyze a concatenated coding scheme, where the outer code is…
The presence of low dimensional chaos in the protein secondary structures, using the binary coded $\alpha$-helices and $\beta$-sheet motifs, has been investigated. In order to analyse symbolic DNA/RNA sequences the assignment, based on 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…
Accurate prediction of RNA properties, such as stability and interactions, is crucial for advancing our understanding of biological processes and developing RNA-based therapeutics. RNA structures can be represented as 1D sequences, 2D…
We use our model of the small scale structure on cosmic strings to develop further the result of Siemens, Olum, and Vilenkin that the gravitational radiation length scale on cosmic strings is smaller than the previously assumed $\Gamma G\mu…
Consider the network of all secondary structures of a given RNA sequence, where nodes are connected when the corresponding structures have base pair distance one. The expected degree of the network is the average number of neighbors, where…
A considerable fraction of Galactic supernova remnants (SNRs) characterize flat spectral indices ($\alpha<0.5$). There are several explanations of the flat radio spectra of SNRs in the present literature. The most of models involve a…
We extend recent methods for parametric sequence alignment to the parameter space for scoring RNA folds. This involves the construction of an RNA polytope. A vertex of this polytope corresponds to RNA secondary structures with common…
Semiflexible polymers are widely used as a paradigm for understanding structural phases in biomolecules including folding of proteins. Here, we compare bead-spring and bead-stick variants of coarse-grained semiflexible polymer models that…
A theoretical investigation is made of acoustic wave propagation in a periodically stubbed waveguide. In general the waveguide segments and stubs are made of different materials. The acoustic wave in such a system has two independent…
An intrinsic branching structure within the transient random walk on a strip in a random environment is revealed. As applications, which enables us to express the hitting time explicitly, and specifies the density of the absolutely…
For sufficiently nice families of semigroups and monoids, the structure theorem for sets of length states that the length set of any sufficiently large element is an arithmetic sequence with some values omitted near the ends. In this paper,…
We investigate the mechanical stability of a segment of DNA wrapped around a histone in the nucleosome configuration. The assumption underlying this investigation is that the proper model for this packaging arrangement is that of an elastic…
We investigate the short, medium, and long-range structure of soft disk configurations for a wide range of area fractions and simulation protocols by converting the real-space spectrum of volume fraction fluctuations for windows of width…
In this paper we study abstract shapes of $k$-noncrossing, $\sigma$-canonical RNA pseudoknot structures. We consider ${\sf lv}_k^{\sf 1}$- and ${\sf lv}_k^{\sf 5}$-shapes, which represent a generalization of the abstract $\pi'$- and…
This paper studies reconstruction of strings based upon their substrings spectrum. Under this paradigm, it is assumed that all substrings of some fixed length are received and the goal is to reconstruct the string. While many existing works…
We extend an hypergraph representation, introduced by Finkelstein and Roytberg, to unify dynamic programming algorithms in the context of RNA folding with pseudoknots. Classic applications of RNA dynamic programming energy minimization,…
RNA design shows growing applications in synthetic biology and therapeutics, driven by the crucial role of RNA in various biological processes. A fundamental challenge is to find functional RNA sequences that satisfy given structural…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
The distribution of GRB durations is bimodal, but there is little additional evidence to support the division of GRBs into short and long classes. Based on simple hardness ratios, several studies have shown a tendency for longer GRBs to…