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The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
An existing conjecture states that the Shannon mutual information contained in the ground state wavefunction of conformally invariant quantum chains, on periodic lattices, has a leading finite-size scaling behavior that, similarly as the…
Cyclic codes are an interesting subclass of linear codes and have been used in consumer electronics, data transmission technologies, broadcast systems, and computer applications due to their efficient encoding and decoding algorithms. In…
Proteins are linear molecular chains that often fold to function. The topology of folding is widely believed to define its properties and function, and knot theory has been applied to study protein structure and its implications. More that…
Information theoretic analysis of genetic languages indicates that the naturally occurring 20 amino acids and the triplet genetic code arose by duplication of 10 amino acids of class-II and a doublet genetic code having codons NNY and…
We interpret the correlation over five orders of magnitude between high frequency and low frequency in a quasi-periodic oscillations (QPO) found by Psaltis, Belloni & van der Klis (1999) for black hole (BH), neutron star (NS) systems and…
Background Synonymous codon choice is mainly affected by mutation and selection. For the majority of genes within a genome, mutational pressure is the major driving force, but selective strength can be strong and dominant for specific set…
Shannon entropy is widely used to measure the complexity of DNA sequences but suffers from saturation effects that limit its discriminative power for long uniform segments. We introduce a novel metric, the entropy rank ratio R, which…
Models of codon evolution are commonly used to identify positive selection. Positive selection is typically a heterogeneous process, i.e., it acts on some branches of the evolutionary tree and not others. Previous work on DNA models showed…
The physical origin of frequency dependence in elastic constants, which are often found in an ultrasound propagation in filled skutterudites and clathrate compounds, is investigated theoretically. This dependence arises from a coupling…
Magnons are elementary excitations in magnetic materials and undergo nonlinear multimode scattering processes at large input powers. In experiments and simulations, we show that the interaction between magnon modes of a confined magnetic…
We propose a systematic study of Bose-Einstein correlations between identical hadrons coming from different W decays. Experimentally accessible signatures of these correlations as well as of possible color reconnection effects are discussed…
Exotic quarkonia are candidates to new types of hadrons including four quarks or gluonic degrees of freedom as constituents, the latter being a unique feature of QCD. We review recent developments in nonrelativistic EFTs to describe exotic…
We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…
In this paper, we present an application of the Shannon entropy in the case of the planar (non-restricted) four-body problem. Specifically, the Kepler-60 extrasolar system is being investigated with a primary interest in the resonant…
The mass spectra of nucleon resonances with spin 1/2, 3/2, and 5/2 are systematically studied in the constituent quark model with meson-quark coupling, which is inspired by the spontaneous breaking of chiral symmetry of QCD. The meson-quark…
The subject of the present study is the double-layer square-lattice system with the intralayer phonon modulations. We investigate the superconducting and excitonic pairings, as well as their coexistence, as functions of various physical…
The rules that specify how the information contained in DNA codes amino acids, is called "the genetic code". Using a simplified version of the Penna nodel, we are using computer simulations to investigate the importance of the genetic code…
The mechanism of spin-phonon coupling in high-T$_C$ copper oxides is explored from band calculations on La$_{(2-x)}$Sr$_x$CuO$_4$ and HgBa$_2$CuO$_4$ systems. The LMTO band calculations, based on the local density approximation, are made…
The width (W), root mean squared amplitude (Rs) of lower and upper kHz quasi-periodic oscillations (QPOs) from accreting neutron stars vary with frequency. Similarly, the QPO frequency varies with the source count rate (S). Hence, the…