Related papers: Writhe formulas and antipodal points in plectonemi…
Inspired by how certain proteins "sense" knots and entanglements in DNA molecules, here we ask if there exist local geometric features that may be used as a read-out of the underlying topology of generic polymers. We perform molecular…
The essential elements in the construction of the couplings of vector multiplets to supergravity using the conformal approach are repeated. This approach leads automatically to the basic quantities on which the symplectic transformations,…
DNA nanoparticles with three-fold coordination have been observed to self-assemble in experiment into a network equivalent to the hexagonal (6.6.6) tiling, and a network equivalent to the 4.8.8 Archimedean tiling. Both networks are built…
The paper deals with ring extensions $R\subseteq S$ and their lattices $[R,S]$ of subextensions and is mainly devoted to FCP extensions (extensions whose lattices are Artinian and Noetherian). The object of the paper is the introduction and…
The macromolecules that encode and translate information in living systems, DNA and RNA, exhibit distinctive structural asymmetries, including homochirality or mirror image asymmetry and $3' - 5'$ directionality, that are invariant across…
The quaternion Fourier transform (QFT), a generalization of the classical 2D Fourier transform, plays an increasingly active role in particular signal and colour image processing. There tends to be an inordinate degree of interest placed on…
Besides mathematical interest, knots and knot theory have important applications in physics, chemistry, and biology. Stasiak and colleagues devised a constructive method for a knot "energy" using a Metropolis Monte Carlo algorithm to…
Let $n$ be any natural number. Let $K$ be any $n$-dimensional knot in $S^{n+2}$. We define a supersymmetric quantum system for $K$ with the following properties. We firstly construct a set of functional spaces (spaces of fermionic \{resp.…
The windowed quadratic phase Fourier transform (WQPFT) combines the localization capabilities of windowed transforms with the phase modulation structure of the quadratic phase Fourier transform (QPFT). This paper investigates fundamental…
This paper introduces a new systematic algorithm for constructing periodic Euclidean weaving diagrams with combinatorial arguments. It is shown that such a weaving diagram can be considered as a specific type of four-regular periodic planar…
In [2], while studying a relevant class of polyominoes that tile the plane by translation, i.e., double square polyominoes, the authors found that their boundary words, encoded by the Freeman chain coding on a four letters alphabet, have…
Multistep denaturation in a short circular DNA molecule is analyzed by a mesoscopic Hamiltonian model which accounts for the helicoidal geometry. Computation of melting profiles by the path integral method suggests that stacking…
Mechanical properties of nucleic acids play an important role in many biological processes which often involve physical deformations of these molecules. At sufficiently long length scales (say above $\sim 20-30$ base pairs) the mechanics of…
Degeneracy is a salient feature of genetic codes, because there are more codons than amino acids. The conventional table for genetic codes suffers from an inability of illustrating a symmetrical nature among genetic base codes. In fact,…
The role of the topology and its relation with the geometry of biopolymers under different physical conditions is a nontrivial and interesting problem. Aiming at understanding this issue for a related simpler system, we use Monte Carlo…
We define cylindric generalisations of skew Macdonald functions when one of their parameters is set to zero. We define these functions as weighted sums over cylindric skew tableaux: fixing two integers n>2 and k>0 we shift an ordinary skew…
Three coarse-grained models of the double-stranded DNA are proposed and compared in the context of mechanical manipulation such as twisting and various schemes of stretching. The models differ in the number of effective beads (between two…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete…
Coterm polynomials are introduced by Oztas et al. [a novel approach for constructing reversible codes and applications to DNA codes over the ring $F_2[u]/(u^{2k}-1)$, Finite Fields and Their Applications 46 (2017).pp. 217-234.], which…