Related papers: Genetic code on the dyadic plane
It is shown that the structure of the generalized quadrangle of order two is fully encoded in the properties of the Desargues configuration. A point of the quadrangle is represented by a geometric hyperplane of the Desargues configuration…
The article is devoted to phenomena of symmetries and algebras in matrix presentations of the genetic code. The Kronecker family of the genetic matrices is investigated, which is based on the alphabetical matrix [C A; U G], where C, A, U, G…
This paper develops geographic-style maps containing 2D lattices in all known crystals parameterised by recent complete invariants. Motivated by rigid crystal structures, lattices are considered up to rigid motion and uniform scaling. The…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
We introduce new yet easily accessible codes for elements of $GL_r(A)$ with $A$ the adelic ring of a (dimension one) function field over a finite field. They are linear codes, and coincide with classical algebraic geometry codes when $r=1$.…
We define a general class of models representing natural selection between two alleles. The population size and spatial structure are arbitrary, but fixed. Genetics can be haploid, diploid, or otherwise; reproduction can be asexual or…
For a family $\mathcal{C}$ of properly embedded curves in the 2-dimensional disk $\mathbb{D}^{2}$ satisfying certain uniqueness properties, we consider convex polygons $P\subset \mathbb{D}^{2}$ and define a metric $d$ on $P$ such that…
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…
We give an application of Mumford's theory of canonical theta characteristics to a Diophantine problem in characteristic two. We prove that a smooth plane curve over a global field of characteristic two is defined by the determinant of a…
PhD thesis investigating homological quantum codes derived from curved and higher dimensional geometries. In the first part we will consider closed surfaces with constant negative curvature. We show how such surfaces can be constructed and…
We introduce a formalism for the geometry of eukaryotic cells and organisms.Cells are taken to be star-convex with good biological reason. This allows for a convenient description of their extent in space as well as all manner of cell…
The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…
Background/ Objectives: Resolving the origin of the genetic code is fundamental to understanding how life began its journey out of the chemical world. Since its deciphering some 60 years ago, there is still no general theory of the…
The GC-content is very variable in different genome regions and species but although many hypothesis we still do not know the reason why. Here we show that a relationship exists with the mutation rate, in particular we noticed a new…
Analyzing the computational complexity of evolutionary algorithms for binary search spaces has significantly increased their theoretical understanding. With this paper, we start the computational complexity analysis of genetic programming.…
The underlying structure of the canonical amino acid substitution matrix (aaSM) is examined by considering stepwise improvements in the differential recognition of amino acids according to their chemical properties during the branching…
Using the EXIT chart approach, a necessary and sufficient condition is developed for the local stability of iterative decoding of multi-edge type (MET) doubly-generalized low-density parity-check (D-GLDPC) code ensembles. In such code…
We construct the generic phase diagrams encoding the topologically distinct localized and delocalized phases of noninteracting fermionic quasiparticles for any symmetry class from the tenfold way in one, two, and three dimensions. To this…
An important problem in computational arithmetic geometry is to find changes of coordinates to simplify a system of polynomial equations with rational coefficients. This is tackled by a combination of two techniques, called minimisation and…
The family of Euclidean triangles having some fixed perimeter and area can be identified with a subset of points on a nonsingular cubic plane curve, i.e., an elliptic curve; furthermore, if the perimeter and the square of the area are…