Related papers: The block spectrum of RNA pseudoknot structures
We aim to characterise the spectral distributions of bi-infinite, semi-infinite, and finite aperiodic one-dimensional arrays of subwavelength resonators, constructed by sampling from a finite library of building blocks. By adopting the…
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…
We investigate the origin of the ubiquitous existence of flat bands in the network superstructures of atomic chains, where one-dimensional(1D) atomic chains array periodically. While there can be many ways to connect those chains, we…
The spectral moments of ensembles of sparse random block matrices are analytically evaluated in the limit of large order. The structure of the sparse matrix corresponds to the Erd\"os-Renyi random graph. The blocks are i.i.d. random…
The radioactive decay of unstable nuclei created in the rapid neutron capture process releases a large amount of $\gamma$-rays. When the ejecta are optically thick, these $\gamma$-rays may contribute to an associated kilonova. Once…
For $\alpha \in (1,2]$, the $\alpha$-stable graph arises as the universal scaling limit of critical random graphs with i.i.d. degrees having a given $\alpha$-dependent power-law tail behavior. It consists of a sequence of compact measured…
We construct and study an extended random matrix model of RNA (polymer) folding. A perturbation which acts on all the nucleotides in the chain is added to the action of the RNA partition function. The effect of this perturbation on the…
RNA forms elaborate secondary structures through intramolecular base pairing. These structures perform critical biological functions within each cell. Due to the availability of a polynomial algorithm to calculate the partition function…
We study fundamental spectral properties of random block operators that are common in the physical modelling of mesoscopic disordered systems such as dirty superconductors. Our results include ergodic properties, the location of the…
An $k$-noncrossing RNA structure can be identified with an $k$-noncrossing diagram over $[n]$, which in turn corresponds to a vacillating tableaux having at most $(k-1)$ rows. In this paper we derive the limit distribution of irreducible…
The presence of slipknots in configurations of proteins and DNA has been shown to affect their functionality, or alter it entirely. Historically, polymers are modeled as polygonal chains in space. As an alternative to space curves, we…
Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages,…
A veritable zoo of different knots is seen in the ensemble of looped polymer chains, whether created computationally or observed in vitro. At short loop lengths, the spectrum of knots is dominated by the trivial knot (unknot). The…
In many applications of shape analysis, lengths between some landmarks are constrained. For instance, biomolecules often have some bond lengths and some bond angles constrained, and variation occurs only along unconstrained bonds and…
Laws of electrodynamics constrain scattering cross-sections of resonant objects. Nevertheless, a fundamental bound that expresses how larger that scattering cross-section can be is yet to be found. Approaches based on cascading multiple…
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…
Supernova remnants are believed to be a major source of cosmic-rays in the Galaxy. As their progenitors are commonly found clustered in OB associations, one has to consider the possibility of collective effects in the acceleration process.…
The local minima (inherent structures) of a system and their associated transition links give rise to a network. Here we consider the topological and distance properties of such a network in the context of spin glasses. We use steepest…
Based on first-principles calculations we predict that periodically repeated junctions of armchair graphene nanoribbons of different widths form superlattice structures. In these superlattice heterostructures the width and the energy gap…
With the help of one-dimensional random Potts-like model we study the origins of fine structure observed on differential melting profiles of double-stranded DNA. We assess the effects of sequence arrangement on DNA melting curves through…