Related papers: Evolutionary Dynamics in a Simple Model of Self-As…
We present a comprehensive study on discrete morphological symmetries of dynamical systems, which are commonly observed in biological and artificial locomoting systems, such as legged, swimming, and flying animals/robots/virtual characters.…
Theoretical understanding of evolutionary dynamics in spatially structured populations often relies on non-spatial models. Biofilms are among such populations where a more accurate understanding is of theoretical interest and can reveal new…
Evolution by Natural Selection is a process by which progeny inherit some properties from their progenitors with small variation. These properties are subject to Natural Selection and are called adaptive traits and carriers of the latter…
We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…
We propose a class of evolutionary models that involves an arbitrary exchangeable process as the breeding process and different selection schemes. In those models, a new genome is born according to the breeding process, and then a genome is…
Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at…
A first-principles theory is developed for the general evolution of a key structural characteristic of planar granular systems - the cell order distribution. The dynamic equations are constructed and solved in closed form for a number of…
We considered a {multi-block} molecular model of biological evolution, in which fitness is a function of the mean types of alleles located at different parts (blocks) of the genome. We formulated an infinite population model with selection…
We investigate the selective forces that promote the emergence of modularity in nature. We demonstrate the spontaneous emergence of modularity in a population of individuals that evolve in a changing environment. We show that the level of…
The next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent studies have…
New approach to design a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico is proposed. The approach is based on Genetic Algorithms, enforced by new crossover operators, especially worked out for…
Biological systems must be robust for stable function against perturbations, but robustness alone is not sufficient. The ability to switch between appropriate states (phenotypes) in response to different conditions is essential for…
The central goal of a dynamical theory of evolution is to abstract the mean evolutionary trajectory in the trait space by considering ecological processes at the level of the individual. In this work, we develop such a theory for a new…
We investigate a model of evolutionary dynamics on a smooth landscape which features a ``mutator'' allele whose effect is to increase the mutation rate. We show that the expected proportion of mutators far from equilibrium, when the fitness…
In this work we propose a physical model of organismal evolution, where phenotype, organism life expectancy, is directly related to genotype i.e. the stability of its proteins which can be determined exactly in the model. Simulating the…
The cytoplasm is a heterogeneous mixture containing many types of proteins that self-assemble into a wide variety of complexes. The accuracy and speed of cytoplasmic self-assembly is astonishing because it involves the correct…
Self-assembly is a fundamental concept in biology and of significant interest to nanotechnology. Significant progress has been made in characterizing and controlling the properties of the resulting structures, both experimentally and…
Discrete models have a long tradition in engineering, including finite state machines, Boolean networks, Petri nets, and agent-based models. Of particular importance is the question of how the model structure constrains its dynamics. This…
Differentiating structural evolution from structural development or formation opens many avenues of research. The study particularly advances the chemical and physical sciences, material science, energy science, and chemical engineering. By…
We study the self-assembly behaviour of patchy particles with `protein-like' interactions that can be considered as a minimal model for the assembly of viral capsids and other shell-like protein complexes. We thoroughly explore the…