Related papers: A Unified Theory on Construction and Evolution of …
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…
It has been proposed that the degeneracy of the genetic code,i.e., the phenomenon that different codons (base triplets) of DNA are transcribed into the same amino acid, may be interpreted as the result of a symmetry breaking process. In the…
The codons, sixtyfour in number, are distributed over the coding parts of DNA sequences. The distribution function is the plot of frequency-versus-rank of the codons. These distributions are characterised by parameters that are almost…
In this paper, we generalize the minimum flow decomposition problem (MFD) to incorporate uncertain edge capacities and tackle it from the perspective of robust optimization. In the classical flow decomposition problem, a network flow is…
We propose a model that explains the hierarchical organization of proteins in fold families. The model, which is based on the evolutionary selection of proteins by their native state stability, reproduces patterns of amino acids conserved…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
The previously formulated model for the evolution of the genetic code was shown to clarify why base triplets of some precursor amino acids differ by a single base from product amino acid codons, while others show less homology. First, the…
By starting from the four DNA bases order in the Boolean lattice, a novel Lie Algebra of the genetic code is proposed. Here, the principal partitions of the genetic code table were obtained as equivalent classes of quotient subspaces of the…
The genetic code is the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells. The code defines a mapping between tri-nucleotide sequences,…
The rapid advancement of artificial intelligence in materials science requires data standards and data management practices that can capture the complexity of real-world structures, including surfaces, interfaces, defects, and…
The question of what determines genetic diversity both between and within species has long remained unsolved by the modern evolutionary theory (MET). However, it has not deterred researchers from producing interpretations of genetic…
Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a…
Significant fraction (98.5% in humans) of most animal genomes is non- coding dark matter. Its largely unknown function (1-5) is related to programming (rather than to spontaneous mutations) of accurate adaptation to rapidly changing…
In a letter published in Molecular Biology Evolution [10], Chen and Zhang argue that the variation of the mutation rate along the Escherichia coli genome that we recently reported [3] cannot be evolutionarily optimised. To support this…
Molecular conformation generation, a critical aspect of computational chemistry, involves producing the three-dimensional conformer geometry for a given molecule. Generating molecular conformation via diffusion requires learning to reverse…
The genetic code markup is the assignment of stop codons. The standard genetic code markup ensures the maximum possible stability of genetic information with respect to two fault classes: frameshift and nonsense mutations. There are only…
A model of mutation rate evolution for multiple loci under arbitrary selection is analyzed. Results are obtained using techniques from Karlin (1982) that overcome the weak selection constraints needed for tractability in prior studies of…
Theory predicts rapid genetic drift during invasions, yet many expanding populations maintain high genetic diversity. We find that genetic drift is dramatically suppressed when dispersal rates increase with the population density because…
Biologists have long sought a way to explain how statistical properties of genetic sequences emerged and are maintained through evolution. On the one hand, non-random structures at different scales indicate a complex genome organisation. On…
McNamara and Dall (2011) identified novel relationships between the abundance of a species in different environments, the temporal properties of environmental change, and selection for or against dispersal. Here, the mathematics underlying…