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Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the macronucleus). We continue the…
Present day data allow significant reconsideration of ideas on mechanisms underlying the degeneracy in the genetic code. Here a hypothesis is presented which links the degeneracy to possible conformational alterations in the codon-anticodon…
Within biology, it is of interest to construct DNA complexes of a certain shape. These complexes can be represented through graph theory, using edges to model strands of DNA joined at junctions, represented by vertices. Because guided…
In biology, predicting RNA secondary structures plays a vital role in determining its physical and chemical properties. Although we have powerful energy models to predict them as well as parametric analysis to understand the models…
We present a generic scheme to construct corrected trapezoidal rules with spectral accuracy for integral operators with weakly singular kernels in arbitrary dimensions. We assume that the kernel factorization of the form,…
It has been proposed that the degeneracy of the genetic code,i.e., the phenomenon that different codons (base triplets) of DNA are transcribed into the same amino acid, may be interpreted as the result of a symmetry breaking process. In the…
Recently, due to the genomic sequence analysis in several types of cancer, the genomic data based on {\em copy number profiles} ({\em CNP} for short) are getting more and more popular. A CNP is a vector where each component is a…
The helical coil is ubiquitous in biological and natural systems and often it is the basic form that leads to complex structures. This paper considers the question of its dimensionality in biological information as the helical coil goes…
We use the worm-like chain model to study supercoiling of DNA under tension and torque. The model reproduces experimental data for a much broader range of forces, salt concentrations and contour lengths than previous approaches. Our theory…
Using the fact that every worldsheet is ruled by two (light-cone) copies of worldlines, the recent classification of off-shell supermultiplets of N-extended worldline supersymmetry is extended to construct standard off-shell and also…
The structures of cyclic DNA codes of odd length over the finite rings R=Z_{4}+wZ_{4}, w^{2}=2 and S=Z_{4}+wZ_{4}+vZ_{4}+wvZ_{4},w^{2}=2,v^{2}=v,wv=vw are studied. The links between the elements of the rings R, S and 16 and 256 codons are…
Recent developments in string duality suggest that the string scale may not be irrevocably tied to the Planck scale. Two explicit but unrealistic examples are described where the ratio of the string scale to the Planck scale is arbitrarily…
The biggest challenge when using DNA as a storage medium is maintaining its stability. The relative occurrence of Guanine (G) and Cytosine (C) is essential for the longevity of DNA. In addition to that, reverse complementary base pairs…
We test a simplified, local version of the helix model on two synthetic and two natural proteins, to study its efficiency in predicting the native secondary structure. The results we obtain are very good for the synthetic sequences, poorer…
A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for…
We establish the theoretical foundation of the Wigner superposition field, a quantum field framework for spin-1/2 fermions that exhibit a Wigner doublet -- a discrete quantum number arising from nontrivial representations of the extended…
DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax…
Biological information is not only stored in the digital chemical sequence of double helical DNA, but is also encoded in the mechanical properties of the DNA strands, which can influence biochemical processes involving its readout. For…
The modelling of DNA mechanics under external constraints is discussed. Two analytical models are widely known, but disagree for instance on the value of the torsional modulus. The origin of this embarassing situation is located in the…
The small-scale structure of a string connecting a pair of static sources is explored for the weakly-coupled anisotropic SU(2) Yang-Mills theory in (2+1) dimensions. A crucial ingredient in the formulation of the string Hamiltonian is the…