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Satyabrata Sahoo

Publications and source records attributed to Satyabrata Sahoo.

9 recordsLinked to original sources
arXiv2025

Revisiting subregion holography using OPE blocks

In this short note, we revisit the entanglement wedge representation of AdS$_3$ bulk fields in terms of CFT operator product expansion (OPE) blocks for a general class of blocks. Given a boundary interval and its associated causal diamond, the OPEs involve boundary operators with or without spin, and located either at spacelike or timelike edges of the diamond. Only for a subset of these cases, can the OPE block be dual to a geodesic bulk field. We show that when applied to de Sitter, a suitable combination of Euclidean OPE blocks can represent a dS scalar integrated over the timelike extremal surfaces, which play an important role in defining pseudo-entropy. We also work out some simple higher dimensional examples.

hep-th↗
arXiv2006

Identity Elements of Archaeal tRNA

Features unique to a transfer-RNA are recognized by the corresponding tRNA-synthetase. Keeping this in view we isolate the discriminating features of all archaeal tRNA. These are our identity elements. Further, we investigate tRNA-characteristics that delineate the different orders of archaea.

q-bio.GN↗
arXiv2005

tRNA-isoleucine-tryptophan Composite Gene

Transfer-RNA genes in archaea often have introns intervening between exon sequences. The structural motif at the boundary between exon and intron is the bulge-helix-bulge. Computational investigations of these boundary structures in H. marismortui lead us to propose that tRNA-isoleucine and tRNA-tryptophan genes are co-located. Precise insilico identification of the splice-sites on the bulges at the exon-intron boundaries conduce us to infer that a single intron-containing composite tRNA-gene can give rise to more than one gene produc.

q-bio.GN↗
arXiv2005

Embedded transfer RNA Genes

In euryarchaeal methanogen M.kandleri and in Nanoarchaea N. equitans some of the missing tRNA genes are embedded in others. We argue from bioinformatic evidence that position specific intron splicing is the key behind co-location of these tRNA genes.

q-bio.BM↗
arXiv2005

Positioning Crenarchaeal tRNA-Introns

We precisely position a noncanonical intron in the odd second copy of tRNAAsp(GTC) gene in the newly sequenced crenarchaea S.acidocaldarius. The uniform assortment of some features from normal aspartate tDNA and some from those corresponding to non-standard amino acids conduce us to conjecture it to be a novel tRNA gene, probably coding for a modified aspartate residue. Further we reposition intron in tRNAHis(GUG) gene in P.aerophilum.The BHB motif at the exon-intron boundaries are re-analyzed and found to support our conjectures.

q-bio.GN↗
arXiv2005

Weighted-Codon-Usage Based Phylogeny In Ectocarpales

We analyse forty seven chloroplastid genes of the large subunit of RuBisCO, from the Algal order Ectocarpales, sourced from GenBank. Codon-usage weighted by the nucleotide base bias defines our score called the Codon-Impact-Parameter. This score is used to obtain phylogenetic relations amongst the 47 Ectocarpales. We compare our classification with the ones done earlier.

q-bio.GN↗
arXiv2005

tRNA-alike in Nanoarchaeum equitans ?

The recent algorithm for five split tRNA-genes in N.equitans is new . It locates missing tRNA-trp, tRNA-imet, tRNA-glu and tRNA-his . But the split tRNA-trp(CCA) solution is anomalous ; the tRNA-imet lacks cognition elements for aminoacylation . In view therefore we present here alternate non-split composite solutions for tRNA-trp, tRNA-imet, tRNA-glu and tRNA-his .

q-bio.GN↗
arXiv2001

Evolution: The Case of the Glyceraldehyde-3-Phosphate Dehydrogenase Gene

The enzyme Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) catalyses the decomposition of glucose. The gene that produces the GAPDH is therefore present in a wide class of organisms. We show that for this gene the average value of the fluctuations in nucleotide distribution in the codons, normalized to strand bias, provides a reasonable measure of how the gene has evolved in time.

physics.bio-ph↗