Related papers: Enumerating secondary structures and structural mo…
Three-dimensional protein structures usually contain regions of local order, called secondary structure, such as $\alpha$-helices and $\beta$-sheets. Secondary structure is characterized by the local rotational state of the protein…
Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures are comparatively scarce. We introduce \emph{RiboSphere}, a…
Structured RNA plays many functionally relevant roles in molecular life. Structural information, while required to understand the functional cycles in detail, is challenging to gather. Computational methods promise to complement…
The analytical study of disordered system is usually difficult due to the necessity to perform a quenched average over the disorder. Thus, one may resort to the easier annealed ensemble as an approximation to the quenched system. In the…
Is protein secondary structure primarily determined by local interactions between residues closely spaced along the amino acid backbone, or by non-local tertiary interactions? To answer this question we have measured the entropy densities…
It is the first step for understanding how RNA structure folds from base sequences that to know how its secondary structure is formed. Traditional energy-based algorithms are short of precision, particularly for non-nested sequences, while…
RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary…
Existing state-of-the-art methods that take a single RNA sequence and predict the corresponding RNA secondary-structure are thermodynamic methods. These predict the most stable RNA structure, but do not consider the process of structure…
We discuss the physics of RNA as described by its secondary structure. We examine the static properties of a homogeneous RNA-model that includes pairing and base stacking energies as well as entropic costs for internal loops. For large…
We consider Convolutional Neural Networks (CNNs) with 2D structured features that are symmetric in the spatial dimensions. Such networks arise in modeling pairwise relationships for a sequential recommendation problem, as well as secondary…
By performing a comprehensive study on 1832 segments of 1212 complete genomes of viruses, we show that in viral genomes the hairpin structures of thermodynamically predicted RNA secondary structures are more abundant than expected under a…
In this work, we investigate a challenging problem, which has been considered to be an important criterion in designing codewords for DNA computing purposes, namely secondary structure avoidance in single-stranded DNA molecules. In short,…
We obtain bivariate asymptotics for the number of (unicellular) combinatorial maps (a model of discrete surfaces) as both the size and the genus grow. This work is related to two research topics that have been very active recently:…
The statistics of randomly branching double-folded ring polymers are relevant to the secondary structure of RNA, the large-scale branching of plectonemic DNA (and thus bacterial chromosomes), the conformations of single-ring polymers…
A topological RNA structure is derived from a diagram and its shape is obtained by collapsing the stacks of the structure into single arcs and by removing any arcs of length one. Shapes contain key topological, information and for fixed…
The structural properties of additive binary hard-sphere mixtures are addressed as a follow-up of a previous paper [S. Pieprzyk et al., Phys. Rev. E 101, 012117 (2020)]. The so-called rational-function approximation method and an approach…
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…
We present a systematic understanding of the rotational structure of a long-range (vibrationally highly-excited) diatomic molecule. For example, we show that depending on a quantum defect, the least-bound vibrational state of a diatomic…
We propose a new deterministic methodology to predict RNA sequence and protein folding. Is stem enough for structure prediction? The main idea is to consider all possible stem formation in the given sequence. With the stem loop energy and…
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have…