Related papers: Neutrally Evolving Interlocking Complexity in the …
We simulate neutral evolution of proteins imposing conservation of the thermodynamic stability of the native state in the framework of an effective model of folding thermodynamics. This procedure generates evolutionary trajectories in…
Wagner's modularity inducing problem domain is a key contribution to the study of the evolution of modularity, including both evolutionary theory and evolutionary computation. We study its behavior under classical genetic algorithms. Unlike…
Aspects of cell metabolism are modeled by ordinary differential equations describing the change of intracellular chemical concentrations. There is a correspondence between this dynamical system and a complex network. As in the classic…
The activities and interactions of proteins that govern the cellular response to a signal generate a multitude of protein phosphorylation states and heterogeneous protein complexes. Here, using a computational model that accounts for 307…
The prevalence of multicellular organisms is due in part to their ability to form complex structures. How cells pack in these structures is a fundamental biophysical issue, underlying their functional properties. However, much remains…
We simulate an individual-based model that represents both the phenotype and genome of digital organisms with predator-prey interactions. We show how open-ended growth of complexity arises from the invariance of genetic evolution operators…
In complex systems, feedback loops can build intricate emergent phenomena, so that a description of the whole system cannot be easily derived from the properties of the individual parts. Here we propose that inter-molecular frustration…
A central goal of evolutionary biology is to explain the origins and distribution of diversity across life. Beyond species or genetic diversity, we also observe diversity in the circuits (genetic or otherwise) underlying complex functional…
Active particle systems of interacting self-propelled particles offer a versatile framework for modeling complex systems. When employed to describe aspects of animal behavior, the complexity of animal movement and decision-making often…
One thing that discriminates living things from inanimate matter is their ability to generate similarly complex or non-random architectures in a large abundance. From DNA sequences to folded protein structures, living cells, microbial…
Complex dynamical systems are often modeled as networks, with nodes representing dynamical units which interact through the network's links. Gene regulatory networks, responsible for the production of proteins inside a cell, are an example…
Collective behavior of proteins on biomembranes is usually studied within the spontaneous curvature model. Here we consider an alternative phenomenological approach, which accounts consistently for partial ordering of proteins as well as…
Large sets of genotypes give rise to the same phenotype because phenotypic expression is highly redundant. Accordingly, a population can accept mutations without altering its phenotype, as long as thegenotype mutates into another one on the…
The article seeks to formulate a synergetic law that is posited to be of common physicochemical and biological nature: an evolving system, possessing free energy and elements with chiral asymmetry may change the type of symmetry inside one…
Globular proteins are expected to assume folds with fixed secondary structures, alpha-helices and beta-sheets. Fold-switching proteins challenge this expectation by remodeling their secondary and/or tertiary structures in response to…
Cell reproduction involves replication of diverse molecule species, in contrast to simple replication system with fewer components. Here, we address why such diversity is sustained despite the efficiency of simple replication systems, using…
Biological systems, from cells to organisms, must respond to the ever changing environment in order to survive and function. This is not a simple task given the often random nature of the signals they receive, as well as the intrinsically…
We study a class of evolution models, where the breeding process involves an arbitrary exchangeable process, allowing for mutations to appear. The population size $n$ is fixed, hence after breeding, selection is applied. Individuals are…
Quantum and biological systems are seldom discussed together as they seemingly demand opposing conditions. Life is complex, "hot and wet" whereas quantum objects are small, cold and well controlled. Here, we overcome this barrier with a…
Molecular biology explains function of molecules by their geometrical and electronical structures that are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any…