相关论文: On the structure of RNA branching polytopes
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…
We analyze the structure of DNA molecules of different organisms by using the additive Markov chain approach. Transforming nucleotide sequences into binary strings, we perform statistical analysis of the corresponding "texts". We develop…
We continue our study of symmetries of a class of little string theories of A-type, which are engineered by $N$ parallel M5-branes probing a flat transverse space. Extending the analysis of the companion paper, we discuss the part of the…
Inference of the network structure (e.g., routing topology) and dynamics (e.g., link performance) is an essential component in many network design and management tasks. In this paper we propose a new, general framework for analyzing and…
Rapid determination of molecular structures can greatly accelerate workflows across many chemical disciplines. However, elucidating structure using only one-dimensional (1D) NMR spectra, the most readily accessible data, remains an…
We consider branching particle processes on discrete structures like the hypercube in a random fitness landscape (i.e., random branching/killing rates). The main question is about the location where the main part of the population sits at a…
We characterize the connectivity structure of feed-forward, deep neural networks (DNNs) using network motif theory. To address whether a particular motif distribution is characteristic of the training task, or function of the DNN, we…
We present a bottom-up approach to the question of supersymmetry breaking in the MSSM. Starting with the experimentally measurable low energy supersymmetry breaking parameters which can take any values consistent with present experimental…
RNA molecules are known to form complex secondary structures including pseudoknots. A systematic framework for the enumeration, classification and prediction of secondary structures is critical to determine the biological significance of…
A growing number of RNA sequences are now known to have distributions of multiple stable sequences. Recent algorithms use the list of nucleotides in a sequence and auxiliary experimental data to predict such distributions. Although the…
Motivation: DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures. In this paper we pose the question to what extent sequence- and structure-information correlate. We view this correlation as…
Many computerized methods for RNA-RNA interaction structure prediction have been developed. Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA…
It is a classical result of Stein and Waterman that the asymptotic number of RNA secondary structures is $1.104366 \cdot n^{-3/2} \cdot 2.618034^n$. Motivated by the kinetics of RNA secondary structure formation, we are interested in…
An all-atom model of proteins is used to show that the same sequence of amino acids can have many alternative structures, that are very distant from, and that can be as stable as, the corresponding native structure. Such alternative…
The formalism of the scattering matrix is applied to describe the transmission properties of multilayered structures with deep variations of the refractive index and arbitrary arrangements of the layers. We show that there is an exact…
RNA secondary structures prediction is one of the main issues in bioinformatics. It seeks to elucidate structural conserved regions within a set of RNA sequences. Unfortunately, finding an accurate conserved structure is a very hard task to…
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…
RNA folding prediction remains challenging, but can be also studied using a topological mathematical approach. In the present paper, the mathematical method to compute the topological classification of RNA structures and based on matrix…
An intrinsic multitype branching structure within the transient (1;R)-RWRE is revealed. The branching structure enables us to specify the density of the absolutely continuous invariant measure for the environments seen from the particle and…
Models for RNA secondary structures (the topology of folded RNA) without pseudo knots are disordered systems with a complex state-space below a critical temperature. Hence, a complex dynamical (glassy) behavior can be expected, when…