Related papers: From the Wobble to Reliable Hypothesis
This work gives a mathematical foundation for bifurcation from a stable equilibrium in the genome. We construct idealized dynamics associated with the genome. For this dynamics we investigate the two main bifurcations from a stable…
A great part of the effort in the study of coarse grained models of transcription networks is directed to the analysis of their dynamical features. In this letter, we consider the \emph{equilibrium} properties of such systems, showing that…
In this work it is shown that 20 canonical amino acids (AAs) within genetic code appear to be a whole system with strict AAs positions; more exactly, with AAs ordinal number in three variants; first variant 00-19, second 00-21 and third…
We numerically study the effects of two forms of quenched disorder on the anyons of the toric code. Firstly, a new class of codes based on random lattices of stabilizer operators is presented, and shown to be superior to the standard square…
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…
Monotone Boolean functions are a structurally important class of Boolean functions, but their restricted form imposes strong limitations on achievable nonlinearity. In this paper, we investigate whether evolutionary computation can evolve…
This paper is concerned with conditions for the existence of oscillations in gene regulatory networks with negative cyclic feedback, where time delays in transcription, translation and translocation process are explicitly considered. The…
There is an intrinsic relationship between the molecular evolution in primordial period and the properties of genomes and proteomes of contemporary species. The genomic data may help us understand the driving force of evolution of life at…
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…
All cells respond to changes in both their internal milieu and the environment around them through the regulation of their genes. Despite decades of effort, there remain huge gaps in our knowledge of both the function of many genes (the…
Mechanical properties of nucleic acids play an important role in many biological processes which often involve physical deformations of these molecules. At sufficiently long length scales (say above $\sim 20-30$ base pairs) the mechanics of…
Synthetic biology sets out to implement new functions in cells, and to develop a deeper understanding of biological design principles. In 2000, Elowitz and Leibler showed that by rational design of the reaction network, and using existing…
Based on extensive study of a dynamical systems model of the development of a cell society, a novel theory for stem cell differentiation and its regulation is proposed as the ``chaos hypothesis''. Two fundamental features of stem cell…
The presence of clusters of rare codons is known to negatively impact the efficiency and accuracy of protein production. In this paper, we demonstrate a statistical method of identifying such clusters in the coding sequence of a gene. Using…
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,…
Transcriptional regulation by transcription factors and post-transcriptional regulation by microRNAs constitute two major modes of regulation of gene expression. While gene expression motifs incorporating solely transcriptional regulation…
Motivated by recent experiments on an antibiotic resistance gene, we investigate genetic interactions between synonymous mutations in the framework of exclusion models of translation. We show that the range of possible interactions is…
New developments are presented in the framework of the model introduced by the authors in refs. [1,2] and in which nucleotides as well as codons are classified in crystal bases of the quantum group U_q(sl(2)+sl(2)) in the limit q -> 0. An…
Coupling the control of expression stochasticity (noise) to the ability of expression change (plasticity) can alter gene function and influence adaptation. A number of factors, such as transcription re-initiation, strong chromatin…
We investigate the possibility of encoding multiple solutions of a problem in a single chromosome. The best solution encoded in an individual will represent (will provide the fitness of) that individual. In order to obtain some benefits the…