Related papers: Semi-phenomenological classification models of the…
We define a new problem in comparative genomics, denoted PQ-Tree Search, that takes as input a PQ-tree $T$ representing the known gene orders of a gene cluster of interest, a gene-to-gene substitution scoring function $h$, integer…
Much information is stored in amino acid composition of protein and base composition of DNA. We simulated the evolution of amino acid frequencies and genomic GC content by a linguistic model. It is showed that the evolution of genetic code…
The multinomial coefficient and their recurrence relations from the generalized quantum deformed algebras are examined. Moreover, the $\mathcal{R}(p,q)-$ deformed multinomial probability distribution and the negative $\mathcal{R}(p,q)-$…
We use high-precision spectroscopy and detailed theoretical modelling to determine the form of the coupling between a superconducting phase qubit and a two-level defect. Fitting the experimental data with our theoretical model allows us to…
All known terrestrial proteins are coded as continuous strings of ~20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method…
We have recently showed that it is possible to deal with collections of indistinguishable elementary particles (in the context of quantum mechanics) in a set-theoretical framework by using hidden variables, in a sense. In the present paper…
A quantitative theory on the construction and the evolution of the genetic code is proposed. Through introducing the concept of mutational deterioration (MD) and developing a theoretical formalism on MD minimization we have proved: 1, the…
We axiomatize the molecular-biology reasoning style, show compliance of the standard reference: Ptashne, A Genetic Switch, and present proof-theory-induced technologies to help infer phenotypes and to predict life cycles from genotypes. The…
We use the theory of the quantum group $U_q(gl(2,\RR))$ in order to develop a quantum theory of invariants and show a decomposition of invariants into a Gordan-Capelli series. Higher binary forms are introduced on the basis of braided…
Computer vision-based methods have valuable use cases in precision medicine, and recognizing facial phenotypes of genetic disorders is one of them. Many genetic disorders are known to affect faces' visual appearance and geometry. Automated…
We introduce genetic algorithms as a means to estimate the accuracy required to discriminate among different models using experimental observables. We exemplify the technique in the context of the minimal supersymmetric standard model. If…
This paper deals with quon algebras or deformed oscillator algebras, for which the deformation parameter is a root of unity. We show the interest of such algebras for fractional supersymmetric quantum mechanics, angular momentum theory and…
Considering the increasing number of experimental results in the manufacturing process of quantum dots with different geometries, and the fact that most numerical methods that can be used to investigate quantum dots with non-trivial…
In general, cellular phenotypes, as measured by concentrations of cellular components, involve large degrees of freedom. However, recent measurement has demonstrated that phenotypic changes resulting from adaptation and evolution in…
q-deformed nonlinear field equations are constructed including Klein-Gordon and Maxwell equations. The q-deformation is interpreted as mathematical structure describing specific nonlinearity for which frequency of vibration exponentially…
Developing models that are capable of answering questions of the form "How would x change if y had been z?'" is fundamental to advancing medical image analysis. Training causal generative models that address such counterfactual questions,…
We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…
The aim of these two papers (I and II) is to try to give fundamental concepts of quantum kinematics to q-deformed quantum spaces. Paper I introduces the relevant mathematical concepts. A short review of the basic ideas of q-deformed…
In the present work, 16 genetic code doublets and their cognate amino acids in the genetic code are fitted into a polyhedron model. Based on the structural regularity in nucleobases, and by using a series of common-sense topological…
We investigate numerical semigroups generated by any quadratic sequence with initial term zero and an infinite number of terms. We find an efficient algorithm for calculating the Ap\'ery set, as well as bounds on the elements of the Ap\'ery…