Related papers: Physical Model for the Evolution of the Genetic Co…
In the framework of the crystal basis model of the genetic code, where each codon is assigned to an irreducible representation of $U_{q \to 0}(sl(2) \oplus sl(2))$, single base mutation matrices are introduced. The strength of the mutation…
The idea of the evolution of the genetic code from the CG to the CGUA alphabet has been developed further. The assumption of the originally triplet structure of the genetic code has been substantiated. The hypothesis of the emergence of…
Determining the different conformational states of a protein and the transition paths between them is key to fully understanding the relationship between biomolecular structure and function. This can be accomplished by sampling protein…
The genetic blueprint for the essential functions of life is encoded in DNA, which is translated into proteins -- the engines driving most of our metabolic processes. Recent advancements in genome sequencing have unveiled a vast diversity…
Biological genotypes do not code directly for phenotypes; developmental physiology is the control layer that separates genomes from capacities ascertained by selection. A key aspect is competency, as cells are not a passive material but…
Migration between different habitats is ubiquitous among biological populations. In this Letter, we study a simple quasispecies model for evolution in two different habitats, with different fitness landscapes, coupled through one-way…
Evolution is the theory that plants and animals today have come from kinds that have existed in the past. Scientists such as Charles Darwin and Alfred Wallace dedicate their life to observe how species interact with their environment, grow,…
A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown…
A codon table is a useful tool for mapping codons to amino acids as they have been assigned by nature. It has become a scientific icon because of the way it embodies our understanding of this natural process and the way it immediately…
In general, cellular phenotypes, as measured by concentrations of cellular components, involve large degrees of freedom. However, recent measurement has demonstrated that phenotypic changes resulting from adaptation and evolution in…
2D display is a fast and economical way of visualizing polymorphism and comparing genomes, which is based on the separation of DNA fragments in two steps, according first to their size and then to their sequence composition. In this paper,…
Rapid advance of experimental techniques provides an unprecedented in-depth view into complex developmental processes. Still, little is known on how the complexity of multicellular organisms evolved by elaborating developmental programs and…
We perform geometrization of genetics by representing genetic information by points of the 4-adic {\it information space.} By well known theorem of number theory this space can also be represented as the 2-adic space. The process of…
The standard genetic code is known to be robust to translation errors and point mutations. We studied how small modifications of the standard code affect its robustness. The robustness was assessed in terms of a proper stability function,…
Having a model and being able to implement open-ended evolutionary systems is important for advancing our understanding of open-endedness. Complex systems science and newest generation high-level programming languages provide intriguing…
Understanding cell fate selection remains a central challenge in developmental biology. We present a class of simple yet biologically-motivated mathematical models for cell differentiation that generically generate oscillations and hence…
Genome rearrangements are evolutionary events that shuffle genomic architectures. Most frequent genome rearrangements are reversals, translocations, fusions, and fissions. While there are some more complex genome rearrangements such as…
Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells…
Given the stochastic nature of gene expression, genetically identical cells exposed to the same environmental inputs will produce different outputs. This heterogeneity has been hypothesized to have consequences for how cells are able to…
What could cause the emergence of non-encoding codons in the course of evolution of the genetic code? Hypothesis of evolution of the genetic code from GC to the AGUC-alphabet account for existence of stop codons.