Related papers: Sequence selection by dynamical symmetry breaking …
In both natural and artificial studies, evolution is often seen as synonymous to natural selection. Individuals evolve under pressures set by environments that are either reset or do not carry over significant changes from previous…
Consider a population of heterogenous agents whose choice behaviors are partially \textit{comparable} according to a given \textit{primitive ordering}.The set of choice functions admissible in the population specifies a \textit{choice…
In this short communication, we shall explore a nonlinear discrete dynamical system that naturally occurs in population systems to describe a transmission of a trait from parents to their offspring. We consider a Mendelian inheritance for a…
We study the dynamics of synthetic molecules whose architectures are generated by space transformations from a point group acting on seed resonators. We show that the dynamical matrix of any such molecule can be reproduced as the left…
Bacteria often develop distinct phenotypes to adapt to environmental stress. In particular, they can produce biofilms, dense communities of bacteria that live in a complex extracellular matrix. Bacterial biofilms provide a safe haven from…
We have discovered a novel transition rule for binary cellular automata (CA) that yields self-replicating structures across two spatial and temporal scales from sparsely populated random initial conditions. Lower-level, shapeshifting…
Evolution is often understood through genetic mutations driving changes in an organism's fitness, but there is potential to extend this understanding beyond the genetic code. We propose that natural products - complex molecules central to…
The continuity of life and its evolution, we proposed, emerge from an interactive group process manifested in networks of interaction. We term this process \textit{survival-of-the-fitted}. Here, we reason that survival of the fitted results…
Simulation models of critical systems often have parameters that need to be calibrated using observed data. For expensive simulation models, calibration is done using an emulator of the simulation model built on simulation output at…
Deterministic many-body systems governed by simple interactions can self-organize into macroscopic patterns, and the determinants of long-time behavior are assumed to be encoded in the initial configuration. Here we show that predictability…
The fields of Origin of Life and Artificial Life both question what life is and how it emerges from a distinct set of "pre-life" dynamics. One common feature of most substrates where life emerges is a marked shift in dynamics when…
Mathematical models play an increasingly important role in the interpretation of biological experiments. Studies often present a model that generates the observations, connecting hypothesized process to an observed pattern. Such generative…
Protein sequences are believed to have been selected to provide the stability of, and reliable renaturation to, an encoded unique spatial fold. In recently proposed theoretical schemes, this selection is modeled as ``minimal frustration,''…
This study introduces a novel theoretical framework, the Stacked Autoencoder Evolution Hypothesis, which proposes that biological evolutionary systems operate through multi-layered self-encoding and decoding processes, analogous to stacked…
We present a two-species population model in a well-mixed environment where the dynamics involves, in addition to birth and death, changes due to environmental factors and inter-species interactions. The novel dynamical components are…
The evolution of enzyme production is studied analytically using ideas of the group selection theory for the evolution of altruistic behavior. In particular, we argue that the mathematical formulation of Wilson's structured deme model ({\it…
Genetic information and environmental factors determine the path of an individuals life and therefore, the evolution of its entire species. We have succeeded in proposing and studying a model that captures this idea. In our model, a…
As an attempt to understand the homochirality of organic molecules in life, a chemical reaction model is proposed where the production of chiral monomers from achiral substrate is catalyzed by the polymers of the same enatiomeric type. This…
Machine learning techniques including neural networks are popular tools for materials and chemical scientists with applications that may provide viable alternative methods in the analysis of structure and energetics of systems ranging from…
Disordered systems theory provides powerful tools to analyze the generic behaviors of highdimensional systems, such as species-rich ecological communities or neural networks. By assuming randomness in their interactions, universality…