Related papers: Enumerating secondary structures and structural mo…
Co-optimizing mRNA sequences for both codon optimality and secondary structure is crucial for producing stable and efficacious mRNA therapeutics. Codon optimization, which adjusts nucleotide sequences to enhance translational efficiency,…
Shapes of interacting RNA complexes are studied using a filtration via their topological genus. A shape of an RNA complex is obtained by (iteratively) collapsing stacks and eliminating hairpin loops. This shape-projection preserves the…
We consider a simple model for the unfolding of RNA tertiary structure under dynamic loading. The opening of such a structure is regarded as a two step process, each corresponding to the overcoming of a single energy barrier. The resulting…
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…
Understanding the base pairing of an RNA sequence provides insight into its molecular structure.By mining suboptimal sampling data, RNAprofiling 1.0 identifies the dominant helices in low-energy secondary structures as features, organizes…
The tertiary structures of functional RNA molecules remain difficult to decipher. A new generation of automated RNA structure prediction methods may help address these challenges but have not yet been experimentally validated. Here we apply…
The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well…
Various specifiable combinatorial structures, with d extensive parameters, can be exactly sampled both by the recursive method, with linear arithmetic complexity if a heavy preprocessing is performed, or by the Boltzmann method, with…
The secondary structure of ribonucleic acid (RNA) is more stable and accessible in the cell than its tertiary structure, making it essential for functional prediction. Although deep learning has shown promising results in this field,…
Background: Genotype-phenotype maps provide a meaningful filtration of sequence space and RNA secondary structures are particular such phenotypes. Compatible sequences i.e.~sequences that satisfy the base pairing constraints of a given RNA…
Structural prediction has long been considered critical in RNA research, especially following the success of AlphaFold2 in protein studies, which has drawn significant attention to the field. While recent advances in machine learning and…
In a DNA sequence, we have the celebrated Watson-Crick complement $\overline{T}=A$, $\overline{A}=T$, $\overline{C}=G$, and $\overline{G}=C$. Given an integer $m\ge 2$, a secondary structure in a DNA sequence refers to the existence of two…
The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy Landscape Theory indicates that it is much easier to find sequences that satisfy the "Principle of Minimal…
In cond-mat/9907125 the low-temperature behavior of a model for RNA secondary structure was studied. It is claimed that the model exhibits a breaking of the replica symmetry, since the width of the distribution P(q) of overlaps may converge…
Simulated nucleotide sequences are widely used in theoretical and empirical molecular evolution studies. Conventional simulators generally use fixed parameter time-homogeneous Markov model for sequence evolution. In this work, we use the…
This contribution focuses on the fascinating RNA molecule, its sequence-dependent folding driven by base-pairing interactions, the interplay between these interactions and natural evolution, and its multiple regulatory roles. The four of us…
Myriad viruses use positive-strand RNA molecules as their genomes. Far from being only a repository of genetic material, viral RNA performs numerous other functions mediated by its physical structure and chemical properties. In this…
The formation of a viral capsid -- the highly-ordered protein shell that surrounds the genome of a virus -- is the canonical example of self-assembly. The capsids of many positive-sense RNA viruses spontaneously assemble from in vitro…
We resolve two conjectures of Black-Drellich-Tymoczko about the numbers of valid plane trees for given primary sequences.
Functional or non-coding RNAs are attracting more attention as they are now potentially considered valuable resources in the development of new drugs intended to cure several human diseases. The identification of drugs targeting the…