Related papers: The block spectrum of RNA pseudoknot structures
Complex networks have been mostly characterized from the point of view of the degree distribution of their nodes and a few other motifs (or modules), with a special attention to triangles and cliques. The most exotic phenomena have been…
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Consider two random strings having the same length and generated by an iid sequence taking its values uniformly in a fixed finite alphabet. Artificially place a long constant block into one of the strings, where a constant block is a…
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Some constructions and bounds on the sizes of semiovals contained in the Hermitian curve are given. A construction of an infinite family of 2-blocking sets of the Hermitian curve is also presented.
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Using data from contact maps of the DNA-polymer of $E. Coli$ (at kilobase pair resolution) as an input to our model, we introduce cross-links between monomers in a bead-spring model of a ring polymer at very specific points along the chain.…
Nucleic acids are highly deformable helical molecules constantly stretched, twisted and bent in their biological functioning. Single molecule experiments have shown that double stranded (ds)-RNA and standard ds-DNA have opposite…
We introduce a compact pangenome representation based on an optimal segmentation concept that aims to reconstruct founder sequences from a multiple sequence alignment (MSA). Such founder sequences have the feature that each row of the MSA…
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An essential quantity to ensure evolvability of populations is the navigability of the genotype space. Navigability relies on the existence of sufficiently large genotype networks, that is ensembles of sequences with the same phenotype that…
We analyze the spectral properties of the high-dimensional random geometric graph $G(n, d, p)$, formed by sampling $n$ i.i.d vectors $\{v_i\}_{i=1}^{n}$ uniformly on a $d$-dimensional unit sphere and connecting each pair $\{i,j\}$ whenever…
We derived simple polynomial equations to determine the entire resonance spectra of split ring structures. For double stacking split rings made with flat wires, we showed that the resonance frequency depends linearly on the ring-ring…
We investigate the quantum spectrum and Gamma structure for projective bundles, blow-ups, and standard flips. After restricting the quantum multiplication to the exceptional curve direction, we obtain a decomposition of the quantum…
The functions of RNA pseudoknots (PKs), which are minimal tertiary structural motifs and an integral part of several ribozymes and ribonucleoprotein complexes, are determined by their structure, stability and dynamics. Therefore, it is…