Related papers: DNA coding and G\"odel numbering
DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce…
In this paper, we propose the Neural Knowledge DNA, a framework that tailors the ideas underlying the success of neural networks to the scope of knowledge representation. Knowledge representation is a fundamental field that dedicate to…
The human genome contains repetitive DNA at different level of sequence length, number and dispersion. Highly repetitive DNA is particularly rich in homo-- and di--nucleotide repeats, while middle repetitive DNA is rich of families of…
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…
The conception of multi-alphabetical genetics is represented. Matrix forms of the representation of the multi-level system of molecular-genetic alphabets have revealed algebraic properties of this system. These properties are connected with…
This paper makes a number of connections between life and various facets of genetic and evolutionary algorithms research. Specifically, it addresses the topics of adaptation, multiobjective optimization, decision making, deception, and…
This work proposes a markovian memoryless model for the DNA that simplifies enormously the complexity of it. We encode nucleotide sequences into symbolic sequences, called words, from which we establish meaningful length of words and group…
Neural codes appear efficient. Naturally, neuroscientists contend that an efficient process is responsible for generating efficient codes. They argue that natural selection is the efficient process that generates those codes. Although…
A new family of compound Poisson distribution functions from statistical linguistic is used to study the n-tuples and nucleotide composition features of DNA sequences. The relative frequency distribution of the 6-tuples and 7- tuples…
In many situations, the gene expression signature is a unique marker of the biological state. We study the modification of the gene expression distribution function when the biological state of a system experiences a change. This change may…
A fundamental design rule that nature has developed for biological machines is the intimate correlation between motion and function. One class of biological machines is molecular motors in living cells, which directly convert chemical…
In a certain way, this paper presents the continuation of the previous one which discussed the harmonic structure of the genetic code (Rakocevic, 2004). Several new harmonic structures presented in this paper, through specific unity and…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
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…
The genetic code is profoundly shaped by an origin in ancient RNA-mediated interactions, needing an extended development to reach the Standard Genetic Code (SGC). That development can serially use RNA specificities, a ribonucleopeptide…
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,…
A new version of DNA walks, where nucleotides are regarded unequal in their contribution to a walk is introduced, which allows us to study thoroughly the "fine structure" of nucleotide sequences. The approach is based on the assumption that…
We apply the theory of learning to physically renormalizable systems in an attempt to develop a theory of biological evolution, including the origin of life, as multilevel learning. We formulate seven fundamental principles of evolution…
In this paper we investigate a neural network model in which weights between computational nodes are modified according to a local learning rule. To determine whether local learning rules are sufficient for learning, we encode the network…
The structure of the genetic code is discussed in formal terms. A rectangular table of the code ("the code matrix"), whose properties reveal its arithmetical content tagged with the information symbols in several notations. New parameters…