Related papers: Genetic recombination as a Generalised Gradient Fl…
Randomness is one of the important key concepts of statistics. In epidemiology or medical science, we investigate our hypotheses and interpret results through this statistical randomness. We hypothesized by imposing some conditions to this…
Gene assembly in ciliates is an extremely involved DNA transformation process, which transforms a nucleus, the micronucleus, to another functionally different nucleus, the macronucleus. In this paper we characterize which loop recombination…
Recurrence networks are a novel tool of nonlinear time series analysis allowing the characterisation of higher-order geometric properties of complex dynamical systems based on recurrences in phase space, which are a fundamental concept in…
Recursive permutations whose cycles are the classes of a decidable equivalence relation are studied; the set of these permutations is called $\mathrm{Perm}$, the group of all recursive permutations $\mathcal{G}$. Multiple equivalent…
Populations evolving under the joint influence of recombination and resampling (traditionally known as genetic drift) are investigated. First, we summarise and adapt a deterministic approach, as valid for infinite populations, which assumes…
In his 2011 work, Maas has shown that the law of any time-reversible continuous-time Markov chain with finite state space evolves like a gradient flow of the relative entropy with respect to its stationary distribution. In this work we show…
We provide a general construction of quantum generalized master equations with memory kernel leading to well defined, that is completely positive and trace preserving, time evolutions. The approach builds on an operator generalization of…
We consider the general properties of the replicator dynamical system from the standpoint of its evolution and stability. Vector field analysis as well as spectral properties of such system has been studied. Lyaponuv function for…
Classical systems can be entangled. Entanglement is defined by coincidence correlations. Quantum entanglement experiments can be mimicked by a mechanical system with a single conserved variable and 77.8% conditional efficiency. Experiments…
A generic rectangulation is a partition of a rectangle into finitely many interior-disjoint rectangles, such that no four rectangles meet in a point. In this work we present a versatile algorithmic framework for exhaustively generating a…
Gene gains and losses have shaped the gene repertoire of species since the universal last common ancestor to species today. Genes in extant species were gained at different historical times via de novo creation of new genes, duplication of…
A ubiquitous feature of quantum mechanical theories is the existence of states of superposition. This is expected to be no different for a quantum gravity theory. Guided by this consideration and others we consider a framework in which…
The classical binomial process has been studied by \citet{jakeman} (and the references therein) and has been used to characterize a series of radiation states in quantum optics. In particular, he studied a classical birth-death process…
We define and analyze a coalescent process as a recursive box-filling process whose genealogy is given by an ancestral time-reversed, time-inhomogeneous Bienyam\'{e}-Galton-Watson process. Special interest is on the expected size of a…
It is shown that a general two-component feedback loop can be viewed as a deformed Hamiltonian system. Some of the implications of using ideas from theoretical physics to study biological processes are discussed.
In the presence of a neighboring atom, electron-ion recombination can proceed resonantly via excitation of an electron in the atom, with subsequent relaxation through radiative decay. It is shown that this two-center dielectronic process…
We describe a scheme for constructing quantum mechanics in which a quantum system is considered as a collection of open classical subsystems. This allows using the formal classical logic and classical probability theory in quantum…
Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by…
We describe an implementation of a genetic algorithm on partially commutative groups and apply it to the double coset search problem on a subclass of groups. This transforms a combinatorial group theory problem to a problem of combinatorial…
We consider various modeling levels for spatially homogeneous chemical reaction systems, namely the chemical master equation, the chemical Langevin dynamics, and the reaction-rate equation. Throughout we restrict our study to the case where…