Related papers: Sequence selection by dynamical symmetry breaking …
The directed polymerization of actin networks is an essential element of many biological processes, including cell migration. Different theoretical models considering the interplay between the underlying processes of polymerization, capping…
Sweepstakes reproduction may be generated by chance matching of reproduction with favorable environmental conditions. Gene genealogies generated by sweepstakes reproduction are in the domain of attraction of multiple-merger coalescents…
Self-closing assembly is prone to polymorphism due to thermally-excited bending fluctuations, which permit the formation of off-target assemblies at the point of self-closure. One way to overcome this source of polymorphism is to use…
In this work, we discovered a fundamental connection between selection for protein stability and emergence of preferred structures of proteins. Using standard exact 3-dimensional lattice model we evolve sequences starting from random ones…
In silico tools are important for generating novel hypotheses and exploring alternatives in de novo metabolic pathway design. However, while many computational frameworks have been proposed for retrobiosynthesis, few successful examples of…
The aim of this review is to present and analyze the probabilistic models of mathematical phylogenetics which have been intensively used in recent years in biology as the cornerstone of attempts to infer and reconstruct the ancestral…
A system of nested dichotomies is a method of decomposing a multi-class problem into a collection of binary problems. Such a system recursively splits the set of classes into two subsets, and trains a binary classifier to distinguish…
Analysis of molecular scale interactions and chemical structure offers an enormous opportunity to tune material properties for targeted applications. However, designing materials from molecular scale is a grand challenge owing to the…
Recent computational experiments have demonstrated the spontaneous emergence of self-replicating programs across universal automata, artificial chemistries, and self-modifying code systems. Remarkably, these results arise without explicit…
Directed polymers on 1+1 dimensional lattices coupled to a heat bath at temperature $T$ are studied numerically for three ensembles of the site disorder. In particular correlations of the disorder as well as fractal patterning are…
Non-equilibrium selection pressures were proposed for the formation of oligonucleotides with rich functionalities encoded in their sequences, such as catalysis. Since phase separation was shown to direct various chemical processes, we ask…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
The dominant paradigm in origin of life research is that of an RNA world. However, despite experimental progress towards the spontaneous formation of RNA, the RNA world hypothesis still has its problems. Here, we introduce a novel…
Phase separation, the spontaneous segregation of density, is a ubiquitous phenomenon observed across diverse physical and biological systems. Within a crowd of motile elements, active phase separation emerges from the interplay of activity…
Active living matter continuously creates and annihilates topological defects in a process that remains poorly understood. Here, we investigate these dynamics in two distinct active living systems: swarming bacteria and human bronchial…
We revisit the classical population genetics model of a population evolving under multiplicative selection, mutation and drift. The number of beneficial alleles in a multi-locus system can be considered a trait under exponential selection.…
Self-organization of complex morphological patterns from local interactions is a fascinating phenomenon in many natural and artificial systems. In the artificial world, typical examples of such morphogenetic systems are cellular automata.…
Organisms and ecological groups accumulate evidence to make decisions. Classic experiments and theoretical studies have explored this process when the correct choice is fixed during each trial. However, we live in a constantly changing…
We study self-replicating molecules under externally varying conditions. Changing conditions such as temperature variations and/or alterations in the environment's resource composition lead to both non-constant replication and decay rates…
Active systems across scales, ranging from molecular machines to human crowds, are usually modeled as assemblies of self-propelled particles driven by internally generated forces. However, these models often assume memoryless dynamics and…