Related papers: Positioning Crenarchaeal tRNA-Introns
Here we present the results of a large-scale bioinformatic annotation of non-coding RNA loci in 48 avian genomes. Our approach uses probabilistic models of hand-curated families from the Rfam database to infer conserved RNA families within…
This paper is devoted to a new classification of the twenty amino acids based on the heronian (integer) tetrahedron.
The effects of the residual proton-neutron interactions on bandcrossing features are studied by means of shell model calculations for nucleons in a high-j intruder orbital. The presence of an odd-nucleon shifts the frequency of the…
This review summarizes recent advances in our understanding of anomalous transport in spin chains, viewed through the lens of integrability. Numerical advances, based on tensor-network methods, have shown that transport in many canonical…
We explore the roles of the trace anomaly in several hadron properties. We derive the scale invariant expression for the pressure from the gravitational form factors (GFF) of QCD which results in consistent results for the mass and rest…
A representation of the genetic code as a six-dimensional Boolean hypercube is proposed. It is assumed here that this structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition.…
Molecular phylogenetic techniques do not generally account for such common evolutionary events as site insertions and deletions (known as indels). Instead tree building algorithms and ancestral state inference procedures typically rely on…
Mass spectrometry studies of odd-odd light rare-earth nuclei by Orford et al. [Phys. Rev. C 102, 011303(R) (2020)] suggested the existence of new isomers in the neutron rich isotopes $^{162}$Tb and $^{164}$Tb. More recently, Stryjczyk et…
Site-specific recombination on supercoiled circular DNA molecules can yield a variety of knots and catenanes. Twist knots are some of the most common conformations of these products and they can act as substrates for further rounds of…
Nature harbors crystals of dimensionality ($d$) only up to three. Here we introduce the notion of \emph{projected topological branes} (PTBs): Lower-dimensional branes embedded in higher-dimensional parent topological crystals, constructed…
We report the observation of a Twist Grain Boundary (TGB) phase of DNA, a striking motif of three dimensional (3D) equilibrium self-assembly of the DNA tetramer 5'-GTAC-3', a base sequence that is self-complimentary, pairing to form 4-base…
We study the thermodynamic and dynamic behaviors of twist-induced denaturation bubbles in a long, stretched random sequence of DNA. The small bubbles associated with weak twist are delocalized. Above a threshold torque, the bubbles of…
We introduce T-branes, or "triangular branes," which are novel non-abelian bound states of branes characterized by the condition that on some loci, their matrix of normal deformations, or Higgs field, is upper triangular. These…
RNA design aims to find a sequence that folds with highest probability into a designated target structure. However, certain structures are undesignable, meaning no sequence can fold into the target structure under the default (Turner) RNA…
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…
Transcription is the first step of gene expression, in which a particular segment of DNA is copied to RNA by the enzyme RNA polymerase (RNAP). Despite many details of the complex interactions between DNA and RNA synthesis disclosed…
Studying crystal structures of superprotonic phases of alkali metal hydrogen sulfates and selenates, a very unusual phenomenon has been revealed. Dynamically disordered hydrogen atoms with low position occupancies are clearly seen in…
This paper proposes a new mathematical approach to characterize native protein structures based on the discrete differential geometry of tetrahedron tiles. In the approach, local structure of proteins is classified into finite types…
Empirical networked systems are often only partially observed: sampling frames, crawling policies, privacy constraints, and temporal gaps can leave actors and edges unobserved. This complicates robustness and sensitivity analysis because…
Graph neural networks (GNNs) have shown promise in integrating protein-protein interaction (PPI) networks for identifying cancer genes in recent studies. However, due to the insufficient modeling of the biological information in PPI…