Related papers: Positioning Crenarchaeal tRNA-Introns
Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These…
We searched for Tc in a sample of long period variables selected by stellar luminosity derived from Hipparcos parallaxes. Tc, as an unstable s-process element, is a good indicator for the evolutionary status of stars on the asymptotic giant…
BRCA genes, comprising BRCA1 and BRCA2 play indispensable roles in preserving genomic stability and facilitating DNA repair mechanisms. The presence of germline mutations in these genes has been associated with increased susceptibility to…
We perform {\textit ab initio} calculations for the strain-induced formation of non-hexagonal-ring defects in graphene, graphane (planar CH), and graphenol (planar COH). We find that the simplest of such topological defects, the Stone-Wales…
It is well known that transcription can induce torsional stress in DNA, affecting the activity of nearby genes or even inducing structural transitions in the DNA duplex. It has long been assumed that the generation of significant torsional…
Understanding the complex and stochastic nature of Gene Regulatory Networks (GRNs) remains a central challenge in systems biology. Existing modeling paradigms often struggle to effectively capture the intricate, multi-factor regulatory…
The NuSTAR serendipitous survey has already uncovered a large number of Active Galactic Nuclei (AGN), providing new information about the composition of the Cosmic X-ray Background. For the AGN off the Galactic plane, it has been possible…
Following our previous results, which provide evidence for the emergence of a chiral p-wave triplet-pairing component in superconducting Nb upon the adsorption of chiral molecules, we turned to investigate whether such an effect can take…
We study the axial anomaly of Dirac spinors on gravitational instanton backgrounds in the context of nonlinear electrodynamics. In order to do so, we consider Einstein gravity minimally coupled to a recently proposed conformal…
Transcription factors (TFs) exert their regulatory action by binding to DNA with specific sequence preferences. However, different TFs can partially share their binding sequences due to their common evolutionary origin. This `redundancy' of…
Certain retroviruses, including HIV, insert their DNA in a non-random fraction of the host genome via poorly understood selection mechanisms. Here, we develop a biophysical model for retroviral integrations as stochastic and…
The human T cell repertoire is generated by the rearrangement of variable (V), diversity (D) and joining (J) segments on the T cell receptor (TCR) loci. To determine whether the structural ordering of these gene segments on the TCR loci…
In this paper it is shown that within a Combined Genetic Code Table, realized through a combination of Watson-Crick Table and Codon Path Cube it exists, without an exception, a strict distinction between two classes of enzymes…
The relative orientation of successive sheets, i.e. the stacking sequence, in layered two-dimensional materials is central to the electronic, thermal, and mechanical properties of the material. Often different stacking sequences have…
The spatial location of cells within tissues and organs is crucial for the manifestation of their specific functions.Spatial transcriptomics technology enables comprehensive measurement of the gene expression patterns in tissues while…
Comparative genomics methods are widely used to aid the functional annotation of non coding DNA regions. However, aligning non coding sequences requires new algorithms and strategies, in order to take into account extensive rearrangements…
Graph Transformers have recently attracted attention for molecular property prediction by combining the inductive biases of graph neural networks (GNNs) with the global receptive field of Transformers. However, many existing hybrid…
Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…
Graphene flakes placed on hexagonal boron nitride feature in the presence of a magnetic field a complex electronic structure due to a hexagonal moir\'e potential resulting from the van der Waals interaction with the substrate. The slight…
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…