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Search for possible relationships between phylogeny and ontogeny is one of the most important issues in the field of evolutionary developmental biology. By representing developmental dynamics of spatially located cells with gene expression…
Color Appearance Models are biological networks that consist of a cascade of linear+nonlinear layers that modify the linear measurements at the retinal photo-receptors leading to an internal (nonlinear) representation of color that…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
The present paper is devoted to foundations of p-adic modelling in genomics. Considering nucleotides, codons, DNA and RNA sequences, amino acids, and proteins as information systems, we have formulated the corresponding p-adic formalisms…
We consider branching process evolving in i.i.d. random environment. It is assumed that the process is intermediately subcritical. We investigate the initial stage of the evolution of the process given its survival for a long time.
Combining a spatiotemporal, multi-agent based model of a foraging ecosystem with linear, genetically programmed rules for the agents' behaviors results in implicit, endogenous, objective functions and selection algorithms based on "natural…
This paper presents a new type of genetic algorithm for the set covering problem. It differs from previous evolutionary approaches first because it is an indirect algorithm, i.e. the actual solutions are found by an external decoder…
Biological diversity has evolved despite the essentially infinite complexity of protein sequence space. We present a hierarchical approach to the efficient searching of this space and quantify the evolutionary potential of our approach with…
Cells continuously sense their surroundings to detect modifications and generate responses. Very often changes in extracellular concentrations initiate signaling cascades that eventually result in changes in gene expression. Increasing…
Environmental heterogeneity can drive genetic heterogeneity in expanding populations; mutant strains may emerge that trade overall growth rate for an improved ability to survive in patches that are hostile to the wild type. This…
We present a generic threshold model for the co-evolution of the structure of a network and the state of its nodes. We focus on regular directed networks and derive equations for the evolution of the system toward its absorbing state. It is…
We develop an alternative boson sampling model operating on single-photon states followed by linear interferometry and Gaussian measurements. The hardness proof for simulating such continuous-variable measurements is established in two main…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
The advent of neural audio codecs has increased in popularity due to their potential for efficiently modeling audio with transformers. Such advanced codecs represent audio from a highly continuous waveform to low-sampled discrete units. In…
We study the dynamics of genetic code evolution. The model of Vetsigian et al. [1] and Vetsigian [2] uses the mechanism of horizontal gene transfer to demonstrate convergence of the genetic code to a near universal solution. We reproduce…
Evolutionary algorithms usually explore a search space of solutions by means of crossover and mutation. While a mutation consists of a small, local modification of a solution, crossover mixes the genetic information of two solutions to…
The ratio of non-synonymous to synonymous substitutions $\omega(=d_{N}/d_{S})$ has been widely used as a measure of adaptive evolution in protein coding genes. Omega can be defined in terms of population genetics parameters as the fixation…
The genetic code markup is the assignment of stop codons. The standard genetic code markup ensures the maximum possible stability of genetic information with respect to two fault classes: frameshift and nonsense mutations. There are only…
Based on a recently proposed non-equilibrium mechanism for spatial pattern formation [cond-mat/0312366] we study how morphogenesis can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of…
We investigate two representation alternatives for the controllers of teams of cyber agents. We combine these controller representations with different evolutionary algorithms, one of which introduces a novel LLM-supported mutation…