Related papers: A Realistic Model under which the Genetic Code is …
Important aspects of the process of information storage and retrieval in DNA and RNA, and its evolution, are the role of the anticodons and associated $t$RNA's, and correlations between anticodons and amino acids; the degeneracy of the…
Benchmarking optimization algorithms is fundamental for the advancement of computational intelligence. However, widely adopted artificial test suites exhibit limited correspondence with the diversity and complexity of real-world engineering…
Multigrid methods despite being known to be asymptotically optimal algorithms, depend on the careful selection of their individual components for efficiency. Also, they are mostly restricted to standard cycle types like V-, F-, and…
In this work it is shown that 20 canonical amino acids (AAs) within genetic code appear to be a whole system with strict distinction in Genetic Code Table (GCT) into some different quantums: 20, 23, 61 amino acid molecules. These molecules…
Three-dimensional (3D) topological codes offer the advantage of supporting fault-tolerant implementations of non-Clifford gates, yet their performance against realistic noise remains largely unexplored. In this work, we focus on the…
The paper represents three supplements to the source paper, q-bio/0610044 [q-bio.OT], with three new series of harmonic structures of the genetic code, determined by Gauss arithmetical algorithm; by Table of Minimal Adding, as in…
A random-key genetic algorithm is an evolutionary metaheuristic for discrete and global optimization. Each solution is encoded as a vector of N random keys, where a random key is a real number randomly generated in the continuous interval…
We present a computer simulation, which is inspired by Penna model, to help understanding the effect of genetic coding tables on population dynamics. To represent populations we used real and artificial gene sequences in this model. We…
The simplest approximation of interaction potential between amino-acids in proteins is the contact potential, which defines the effective free energy of a protein conformation by a set of amino acid contacts formed in this conformation.…
We study the dynamics of genetic code evolution. The model of Vetsigian et al. [1] and Vetsigian [2] uses the mechanism of horizontal gene transfer to demonstrate convergence of the genetic code to a near universal solution. We reproduce…
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…
In this paper, we propose semiparametric efficient estimators of genetic relatedness between two traits in a model-free framework. Most existing methods require specifying certain parametric models involving the traits and genetic variants.…
Fault tolerant quantum computing methods which work with efficient quantum error correcting codes are discussed. Several new techniques are introduced to restrict accumulation of errors before or during the recovery. Classes of eligible…
We give a formal verification procedure that decides whether a classifier ensemble is robust against arbitrary randomized attacks. Such attacks consist of a set of deterministic attacks and a distribution over this set. The…
The biological distinction between the base positions in the codon, the chemical types of bases (purine and pyrimidine) and their hydrogen bond number have been the most relevant codon properties used in the genetic code analysis. Now,…
Cyclic redundancy check (CRC) codes check if a codeword is correctly received. This paper presents an algorithm to design CRC codes that are optimized for the code-specific error behavior of a specified feedforward convolutional code. The…
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…
Quantum error correction codes are usually designed to correct errors regardless of their physical origins. In large-scale devices, this is an essential feature. In smaller-scale devices, however, the main error sources are often…
Replication of DNA and synthesis of proteins are studied from the view-point of quantum database search. Identification of a base-pairing with a quantum query gives a natural (and first ever) explanation of why living organisms have 4…
A Profile Mixture Model is a model of protein evolution, describing sequence data in which sites are assumed to follow many related substitution processes on a single evolutionary tree. The processes depend in part on different amino acid…