Related papers: On the possible origin and evolution of genetic co…
How robust is the natural genetic code with respect to mistranslation errors? It has long been known that the genetic code is very efficient in limiting the effect of point mutation. A misread codon will commonly code either for the same…
The interactions between DNA, RNA, and proteins are fundamental to biological processes, as illustrated by the central dogma of molecular biology. Although modern biological pre-trained models have achieved great success in analyzing these…
Messenger RNA encodes a sequence of amino acids by using codons. For most amino acids there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for…
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and TADs (topologically-associating domains), to contact domains stabilized by cohesin and CTCF.…
Living organisms are the most complex, interesting and significant objects regarding all substructures of the universe. Life science is regarded as a science of the 21st century and one can expect great new discoveries in the near futures.…
We propose a physical model to describe the mechanisms of two major scenarios of the genetic code evolution, the codon capture and ambiguous intermediate scenarios, in a consistent manner. We sketch the lowest dimensional version of our…
RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of…
In evolutionary policy search, neural networks are usually represented using a direct mapping: each gene encodes one network weight. Indirect encoding methods, where each gene can encode for multiple weights, shorten the genome to reduce…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
Much information is stored in amino acid composition of protein and base composition of DNA. We simulated the evolution of amino acid frequencies and genomic GC content by a linguistic model. It is showed that the evolution of genetic code…
This paper presents a new type of genetic algorithm for the set covering problem. It differs from previous evolutionary approaches first because it is an indirect algorithm, i.e. the actual solutions are found by an external decoder…
This paper characterizes the inherent power of evolutionary algorithms. This power depends on the computational properties of the genetic encoding. With some encodings, two parents recombined with a simple crossover operator can sample from…
Background: A partially random target selection method was developed to design and produce affinity reagents (target) to any protein query. It is based on the recent concept of Proteomic Code (for review see Biro, 2007 [1]) which suggests…
The RNA inverse folding problem, a key challenge in RNA design, involves identifying nucleotide sequences that can fold into desired secondary structures, which are critical for ensuring molecular stability and function. The inherent…
Evolutionary theorizing resembles building an aircraft while also piloting it; new results change the scaffold for older ideas, requiring revised strategy to remain airborne. A calculated kinetic pathway exists that, under explicit…
The inference of gene regulatory networks (GRNs) is a foundational stride towards deciphering the fundamentals of complex biological systems. Inferring a possible regulatory link between two genes can be formulated as a link prediction…
A central challenge in the origin of life is understanding how catalytic peptide-like polymers and information-bearing nucleic acid-like polymers emerged as an interde-pendent system. This study constructs a primordial cognitive model…
Proteins are macromolecules that perform essential functions in all living organisms. Designing novel proteins with specific structures and desired functions has been a long-standing challenge in the field of bioengineering. Existing…
The aims of this paper are to propose, construct and analyse microscopic kinetic models for the emergence of long chains of RNA from monomeric beta-D-ribonucleotide precursors in prebiotic circumstances. Our theory starts out from similar…
Genetic robustness, the preservation of an optimal phenotype in the face of mutations, is critical to the understanding of evolution as phenotypically expressed genetic variation is the fuel of natural selection. The origin of genetic…