Related papers: A Realistic Model under which the Genetic Code is …
Part 1 of the study intends to show that the universal trend of amino acid gain and loss discovered by Jordan et al. (2005) can be accounted for by the spontaneity of DNA typical damages. These damages lead to replacements of guanine and…
Degeneracy of the genetic code is a biological way to minimize effects of the undesirable mutation changes. Degeneration has a natural description on the 5-adic space of 64 codons $\mathcal{C}_5 (64) = \{n_0 + n_1 5 + n_2 5^2 : n_i = 1, 2,…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
Errors occurring on noisy hardware pose a key challenge to reliable quantum computing. Existing techniques such as error correction, mitigation, or suppression typically separate the error handling from the algorithm analysis and design. In…
Robustness to genetic or environmental disturbances is often considered as a key property of living systems. Yet, in spite of being discussed since the 1950s, how robustness emerges from the complexity of genetic architectures and how it…
This work aims at showing the relevance and the applications possibilities of the Fibonacci sequence, and also its q-deformed or quantum extension, in the study of the genetic code(s). First, after the presentation of a new formula, an…
Degeneracy is a salient feature of genetic codes, because there are more codons than amino acids. The conventional table for genetic codes suffers from an inability of illustrating a symmetrical nature among genetic base codes. In fact,…
Using the crystal basis model of the genetic code, a set of relations between the physical-chemical properties of the amino acids are derived and compared with the experimental data. A prevision for the not yet measured thermodynamical…
Effective and reliable data retrieval is critical for the feasibility of DNA storage, and the development of random access efficiency plays a key role in its practicality and reliability. In this paper, we study the Random Access Problem,…
The surface code is one the most promising alternatives for implementing fault-tolerant, large-scale quantum information processing. Its high threshold for single-qubit errors under stochastic noise is one of its most attrative features. We…
The genetic code is connection between 64 codons, which are building blocks of the genes, and 20 amino acids, which are building blocks of the proteins. In addition to coding amino acids, a few codons code stop signal, which is at the end…
Finding the best configuration of algorithms' hyperparameters for a given optimization problem is an important task in evolutionary computation. We compare in this work the results of four different hyperparameter tuning approaches for a…
The training of molecular models of quantum mechanical properties based on statistical machine learning requires large datasets which exemplify the map from chemical structure to molecular property. Intelligent a priori selection of…
Functions of chemical composition are complex and discrete in nature making it impossible to optimize them with gradient methods. Genetic algorithms, which do not use derivative information, are used to maximize the thermal conductivity of…
It has been repeatedly proposed to expand the scope for SETI, and one of the suggested alternatives to radio is the biological media. Genomic DNA is already used on Earth to store non-biological information. Though smaller in capacity, but…
The choice of crossover and mutation strategies plays a crucial role in the searchability, convergence efficiency and precision of genetic algorithms. In this paper, a novel improved genetic algorithm is proposed by improving the crossover…
We seek to understand the interplay between amino acid sequence and local structure in proteins. Are some amino acids unique in their ability to fit harmoniously into certain local structures? What is the role of sequence in sculpting the…
A two amino acid (hydrophobic and polar) scheme is used to perform the design on target conformations corresponding to the native states of twenty single chain proteins. Strikingly, the percentage of successful identification of the nature…
We propose a computational framework to quantify (measure) and to optimize the reliability of complex systems. The approach uses a graph representation of the system that is subject to random failures of its components (nodes and edges).…
In this paper, we introduce an achievability bound on the frame error rate of random tree code ensembles under a sequential decoding algorithm with a hard computational limit and consider the optimization of the random tree code ensembles…