Related papers: Genetic recombination as a Generalised Gradient Fl…
We propose quantization relationships which would let us describe and solution problems originated by conflicting or cooperative behaviors among the members of a system from the point of view of quantum mechanical interactions. The quantum…
Quantum dynamics can be regarded as a generalization of classical finite-state dynamics. This is a familiar viewpoint for workers in quantum computation, which encompasses classical computation as a special case. Here this viewpoint is…
Genetic algorithms are heuristic optimization techniques inspired by Darwinian evolution. Quantum computation is a new computational paradigm which exploits quantum resources to speed up information processing tasks. Therefore, it is…
In the evolution of a genome, the gene sequence is sometimes rearranged, for example by transposition of two adjacent gene blocks. In biocombinatorics, one tries to reconstruct these rearrangement incidents from the resulting permutation.…
It has been recently shown that collisional models can be used to derive a general form for the master equations which describe the reduced time evolution of a composite multipartite quantum system, whose components "propagate" in an…
The possibility to recover the which-way information, for example in the two slit experiment, is based on a natural but implicit assumption about the position of a particle {\it before} a position measurement is performed on it. This…
The problem of large order behaviour of perturbation theory for quantum mechanical systems is considered. A new approach to it is developed. An explicit mechanism showing the connection between large order recursive relations and classical…
I propose to treat quantum evolution as a stochastic process consisting from a sequence of doubly stochastic matrices, which naturally arise in the generalized quantum evolution. Then it is proved that the law of non-decreasing entropy is…
I discuss classical and quantum recurrence theorems in a unified manner, treating both as generalisations of the fact that a system with a finite state space only has so many places to go. Along the way I prove versions of the recurrence…
Several technological applications require the translation of a protein into a nucleic acid that codes for it (``backtranslation''). The degeneracy of the genetic code makes this translation ambiguous; moreover, not every translation is…
The genealogy at a single locus of a constant size $N$ population in equilibrium is given by the well-known Kingman's coalescent. When considering multiple loci under recombination, the ancestral recombination graph encodes the genealogies…
Consider a mean-reverting equation, generalized in the sense it is driven by a 1-dimensional centered Gaussian process with H\"older continuous paths on $[0,T]$ ($T > 0$). Taking that equation in rough paths sense only gives local existence…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
Systems biology uses large networks of biochemical reactions to model the functioning of biological cells from the molecular to the cellular scale. The dynamics of dissipative reaction networks with many well separated time scales can be…
We consider a stochastic model, called the replicator coalescent, describing a system of blocks of $k$ different types which undergo pairwise mergers at rates depending on the block types: with rate $C_{i,j}$ blocks of type $i$ and $j$…
We study the second law in the context of combinatorial processes, focusing on the mechanisms that give rise to irreversible behavior from an underlying deterministic, invertible, and reversible dynamics.
Gene duplication is a major mechanism through which new genetic material is generated. Although numerous methods have been developed to differentiate the ortholog and paralogs, very few differentiate the "Parent-Daughter" relationship among…
One of the fundamental problems of modern physics is how the classical world, the 2nd Law of Thermodynamics and the whole irreversibility emerges from the quantum reality with reversible evolution. This relates to the problem of measurement…
In rule-based systems, goal-oriented computations correspond naturally to the possible ways that an observation may be explained. In some applications, we need to compute explanations for a series of observations with the same domain. The…
Theory of splicing is an abstract model of the recombinant behaviour of DNAs. In a splicing system, two strings to be spliced are taken from the same set and the splicing rule is from another set. Here we propose a generalised splicing (GS)…