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Crossover is the process of recombining the genetic features of two parents. For many applications where crossover is applied to permutations, relevant genetic features are pairs of adjacent elements, also called edges in the permutation…
Spatial transcriptomics (ST) has emerged as an advanced technology that provides spatial context to gene expression. Recently, deep learning-based methods have shown the capability to predict gene expression from WSI data using ST data.…
The structural parameters of alpha helix and some forms of DNA-structures are determined by methods of algebraic topology. These structures are locally periodic and correspond to the bifurcation point for minimal surfaces given by…
We combined the genetic crossover, which is one of the operations of genetic algorithm, and replica-exchange method in parallel molecular dynamics simulations. The genetic crossover and replica-exchange method can search the global…
DNA dependent RNA polymerase core subunits abb' conserved residues at frequencies most closely matched with codons at stage 10.4-11.1 in code evolution. An excess of acidic residues (stage 2 additions) lowered this estimate, but not by more…
Breakage-Fusion-Bridge cycles in cancer arise when a broken segment of DNA is duplicated and an end from each copy joined together. This structure then `unfolds' into a new piece of palindromic DNA. This is one mechanism responsible for the…
We predict that vertical transport in heterostructures formed by twisted graphene layers can exhibit a unique bistability mechanism. Intrinsically bistable $I$-$V$ characteristics arise from resonant tunneling and interlayer charge…
The existence of bound charge transfer (CT) excitons at the interface of monolayer lateral heterojunctions has been debated in literature, but contrary to the case of interlayer excitons in vertical heterostructure their observation still…
Morphogenetic patterns are highly sophisticated dissipative structures. Are they governed by the same general mechanisms as chemical and hydrodynamic patterns? Turing's symmetry breaking and Wolpert's signalling provide alternative…
In this work we propose a model for DNA double helix within the tight-binding framework that incorporates the helicity of the molecules. We have studied localization properties of three DNAsequences,the periodic poly(dG)-poly(dC) and…
We predict a novel temperature-driven phase transition of DNA below the melting transition. The additional, intermediate phase exists for repetitive sequences, when the two strands have different lengths. In this phase, the excess bases of…
Phylogenomic analyses are subject to bias from compositional convergence and noise from horizontal gene transfer (HGT). Compositional convergence is a likely cause of controversy regarding phylogeny of the SAR11 group of Alphaproteobacteria…
This theory seeks to define species and to explore evolutionary forces and genetic elements in speciation and species maintenance. The theory explains how speciation and species maintenance are caused by natural selection acting on…
In columnar assemblies of helical bio-molecules the azimuthal degrees of freedom, i.e. rotations about the long axes of molecules, may be important in determining the structure of the assemblies especially when the interaction energy…
We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…
Sex chromosomes have evolved repeatedly across the Tree of Life, yet their evolutionary fates differ strikingly. In sharp contrast to mammals and birds with degenerated, stable Y/W chromosomes, in most amphibians, teleosts, non avian…
We study the statistical mechanics of RNA secondary structures designed to have an attraction between two different types of structures as a model system for heteropolymer aggregation. The competition between the branching entropy of the…
Genetic oscillators are present in the cells of many organisms and control several biological processes. The common feature of such oscillators is the presence of a protein which represses the transcription of its own gene. Recently, it has…
T-branes are a non-abelian generalization of intersecting branes in which the matrix of normal deformations is nilpotent along some subspace. In this paper we study the geometric remnant of this open string data for six-dimensional F-theory…
Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture model has stimulated considerable recent…