Related papers: A Unified Theory on Construction and Evolution of …
While many optimization problems work with a fixed number of decision variables and thus a fixed-length representation of possible solutions, genetic programming (GP) works on variable-length representations. A naturally occurring problem…
Phenotype of biological systems needs to be robust against mutation in order to sustain themselves between generations. On the other hand, phenotype of an individual also needs to be robust against fluctuations of both internal and external…
We perform an exhaustive analysis of genome statistics for organisms, particularly extremophiles, growing in a wide range of physicochemical conditions. Specifically, we demonstrate how the correlation between the frequency of amino acids…
The Moran model with recombination is considered, which describes the evolution of the genetic composition of a population under recombination and resampling. There are $n$ sites (or loci), a finite number of letters (or alleles) at every…
Quantum low-density parity-check (QLDPC) codes offer a promising path to low-overhead fault-tolerant quantum computation but lack systematic strategies for exploration. In this Letter, we establish a topological framework for studying the…
We present a genetic algorithm developed (GA) to optimize molecular AF_6 cluster configurations with respect to their energy. The method is based on the Darvin's evolutionary theory: structures with lowest energies survive in a system of…
We present a genetic algorithm for the atomistic design and global optimisation of substitutionally disordered bulk materials and surfaces. Premature convergence which hamper conventional genetic algorithms due to problems with…
The common understanding of protein evolution has been that neutral or slightly deleterious mutations are fixed by random drift, and evolutionary rate is determined primarily by the proportion of neutral mutations. However, recent studies…
The evolutionary origins of structural features in reconstructed gene-regulatory networks (GRNs) remain poorly understood, especially given the random aspects of gene expression. Here, we extend a classical model of GRN evolution to allow a…
The biological theory of adaptive dynamics proposes a description of the long-term evolution of a structured asexual population. It is based on the assumptions of large population, rare mutations and small mutation steps, that lead to a…
In population genetics, mutation rate is often treated as a homogeneous parameter across the genome. Empirical evidence, however, shows systematic variation across genomic contexts associated with chromatin organization and epigenomic…
Using the crystal basis model of the genetic code, a set of relations between the physical-chemical properties of the amino acids are derived and compared with the experimental data. A prevision for the not yet measured thermodynamical…
We study the coupled dynamics of primary and secondary structure formation (i.e. slow genetic sequence selection and fast folding) in the context of a solvable microscopic model that includes both short-range steric forces and and…
We propose a new method for computing Dynamic Mode Decomposition (DMD) evolution matrices, which we use to analyze dynamical systems. Unlike the majority of existing methods, our approach is based on a variational formulation consisting of…
During bouts of evolutionary diversification, such as adaptive radiations, the emerging species cluster around different locations in phenotype space, How such multimodal patterns in phenotype space can emerge from a single ancestral…
A topological approach to the study of genetic recombination, based on persistent homology, was introduced by Chan, Carlsson, and Rabad\'an in 2013. This associates a sequence of signatures called barcodes to genomic data sampled from an…
Living organisms are the most complex, interesting and significant objects regarding all substructures of the universe. Life science is regarded as a science of the 21st century and one can expect great new discoveries in the near futures.…
The dynamics of adaptation is difficult to predict because it is highly stochastic even in large populations. The uncertainty emerges from number fluctuations, called genetic drift, arising in the small number of particularly fit…
In this work it is shown that 20 canonical amino acids (AAs) within genetic code appear to be a whole system with strict AAs positions; more exactly, with AAs ordinal number in three variants; first variant 00-19, second 00-21 and third…
We show that textual analysis of microbial genomes reveal telling footprints of the early evolution of the genomes. The frequencies of word occurrence of random DNA sequences considered as texts in their four nucleotides are expected to…