Related papers: From the Wobble to Reliable Hypothesis
We investigated the error-minimization properties of putative primordial codes that consisted of 16 supercodons, with the third base being completely redundant, using a previously derived cost function and the error minimization percentage…
In biochemical signaling, information is often encoded in oscillatory signals. However, the advantages of such a coding strategy over an amplitude encoding scheme of constant signals remain unclear. Here we study the dynamics of a simple…
We give three new proofs of the triangle inequality in Euclidean Geometry. There seems to be only one known proof at the moment. It is due to properties of triangles, but our proofs are due to circles or ellipses. We aim to prove the…
The presence of celestial companions means that any planet may be subject to three kinds of harmonic mechanical forcing: tides, precession/nutation, and libration. These forcings can generate flows in internal fluid layers, such as fluid…
Heteroclinic cycles are widely used in neuroscience in order to mathematically describe different mechanisms of functioning of the brain and nervous system. Heteroclinic cycles and interactions between them can be a source of different…
The development of a large non-coding fraction in eukaryotic DNA and the phenomenon of the code-bloat in the field of evolutionary computations show a striking similarity. This seems to suggest that (in the presence of mechanisms of code…
We investigate irreversibility and dissipation in single molecules that cooperatively fold/unfold in a two state manner under the action of mechanical force. We apply path thermodynamics to derive analytical expressions for the average…
In a letter published in Molecular Biology Evolution [10], Chen and Zhang argue that the variation of the mutation rate along the Escherichia coli genome that we recently reported [3] cannot be evolutionarily optimised. To support this…
In the nuclei of eukaryotic cells, DNA is packaged through several levels of compaction in an orderly retrievable way that enables the correct regulation of gene expression. The functional dynamics of this assembly involves the unwinding of…
In crystals, molecules thermally vibrate around the periodic lattice sites. Vibrational motions are well understood in terms of phonons, which carry heat and control heat transport. The situation is notably different in disordered solids,…
The problem of the directionality of genome evolution is studied from the information-theoretic view. We propose that the function-coding information quantity of a genome always grows in the course of evolution through sequence duplication,…
We report the first observation of two wobbling bands in $^{183}$Au, both of which were interpreted as the transverse wobbling (TW) band but with different behavior of their wobbling energies as a function of spin. It increases (decreases)…
Most of the DNA that composes a complex organism is non-coding and defined as junk. Even the coding part is composed of genes that affect the phenotype differently. Therefore, a random mutation has an effect on the specimen fitness that…
Although theories regarding the role of sequence-specific DNA resonance in biology have abounded for over 40 years, the published evidence for it is lacking. Here, the authors reasoned that for sustained resonance signaling, the number of…
Imposing a minimum principle in the framework of the so called crystal basis model of the genetic code, we determine the structure of the minimum set of 22 anticodons which allows the translational-transcription for animal mitochondrial…
Using a graph representation of classical logic, the paper shows that the liar or Yablo pattern occurs in every semantic paradox. The core graph theoretic result generalizes theorem of Richardson, showing solvability of finite graphs…
Transitive consistency is an intrinsic property for collections of linear invertible transformations between Euclidean coordinate frames. In practice, when the transformations are estimated from data, this property is lacking. This work…
Given the stochastic nature of gene expression, genetically identical cells exposed to the same environmental inputs will produce different outputs. This heterogeneity has been hypothesized to have consequences for how cells are able to…
The ~4-Mbp basic genome shared by 32 independent isolates of E. coli representing considerable population diversity has been approximated by whole-genome multiple-alignment and computational filtering designed to remove mobile elements and…
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…