Related papers: From the Wobble to Reliable Hypothesis
The importance of the notion of symmetry in physics is well established: could it also be the case for the genetic code? In this spirit, a model for the Genetic Code based on continuous symmetries and entitled the "Crystal Basis Model" has…
The current theory of evolution is almost the one Darwin and Wallace proposed two centuries ago and the following discoveries e.g., Mendelian genetics and neutral mutation theory have not made significant modifications. The current…
Gene expression levels exhibit stochastic variations among genetically identical organisms under the same environmental conditions (called gene expression "noise" or phenotype "fluctuation"). In yeast and Escherichia coli, positive…
We investigate the elasticity of unsupported epithelial monolayer and we discover that unlike a thin solid plate, which wrinkles if geometrically incompatible with the underlying substrate, the epithelium may do so even in absence of the…
We study the nonlinear dynamics of a deformed Deoxyribonucleic acid (DNA) molecular chain which is governed by a perturbed sine-Gordon equation coupled with a linear wave equation representing the lattice deformation. The DNA chain…
Topological entropy has been one of the most difficult to implement of all the entropy-theoretic notions. This is primarily due to finite sample effects and high-dimensionality problems. In particular, topological entropy has been…
Martincorena et al. estimated synonymous diversity ({\theta}s = 2N{\mu}) across 2,930 orthologous gene alignments from 34 Escherichia coli genomes, and found substantial variation among genes in the density of synonymous polymorphisms. They…
The systematics of indices of physico-chemical properties of codons and amino acids across the genetic code are examined. Using a simple numerical labelling scheme for nucleic acid bases, data can be fitted as low-order polynomials of the 6…
We provide a new proof of the elementary geometric theorem on the existence and uniqueness of cyclic polygons with prescribed side lengths. The proof is based on a variational principle involving the central angles of the polygon as…
Evolutionary synthesis models have been used to study the physical properties of unresolved populations in a wide range of scenarios. Unfortunately, their self-consistency are difficult to test and there are some theoretical open questions…
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,…
Odd electrons of benzenoid units and correlation of these electrons having different spins are the main concepts of the molecular theory of graphene. In contrast to the theory of aromaticity, the molecular theory is based on the fact that…
Non-coding RNA sequences play a great role in controlling a number of cellular functions, thus raising the need to understand their complex conformational dynamics in quantitative detail. In this perspective, we first show that single…
A system-level genetic code is a hypothetical genetic code that exclusively or preferentially codes systems of interacting coadapted parts. System-level genetic codes differ from part-level genetic codes in which each discrete part is coded…
A codon table is a useful tool for mapping codons to amino acids as they have been assigned by nature. It has become a scientific icon because of the way it embodies our understanding of this natural process and the way it immediately…
Recent experiments and simulations have demonstrated that proteins can fold on the ribosome. However, the extent and generality of fitness effects resulting from co-translational folding remain open questions. Here we report a genome-wide…
A normally functioning menstrual cycle requires significant crosstalk between hormones originating in ovarian and brain tissues. Reproductive hormone dysregulation may cause abnormal function and sometimes infertility. The inherent…
Experiments on a chain of coupled pendula driven periodically at one end demonstrate the existence of a novel regime which produces an output frequency at an odd fraction of the driving frequency. The new stationary state is then obtained…
The concept of gauge invariance in classical electrodynamics assumes tacitly that Maxwell's equations have unique solutions. By calculating the electromagnetic field of a moving particle both in Lorenz and in Coulomb gauge and directly from…
We report here a new entropic mechanism of protein thermostability due to residual dynamics of rotamer isomerization in native state. All-atom simulations show that Lysines have much greater number of accessible rotamers than Arginines in…