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Register a new userOxygen Channels and Fractal Wave-Particle Duality in the Evolution of Myoglobin and Neuroglobin
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The evolution of terrestrial and aquatic wild type (WT) globins is dominated by changes in two proximate - distal Histidine ligand exit channels, here monitored quantitatively by hydropathic waves. These waves reveal allometric functional features inaccessible to single amino acid stereochemical contact models, and even very large all-atom Newtonian simulations. The evolutionary differences between these features between myoglobin and neuroglobin are related to the two oxidation channels through hydropathic wave analysis, which identifies subtle interspecies functional differences inaccessible to traditional size and metabolic scaling studies. Our analysis involves dynamic synchronization of allometric interactions across entire globins.
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The complementary wave and particle character of quantum objects (or quantons) was pointed out by Niels Bohr. This wave-particle duality, in the context of the two-slit experiment, is now described not just as two extreme cases of wave and particle characteristics, but in terms of quantitative measures of these natures. These measures of wave and particle aspects are known to follow a duality relation. A very simple and intuitive derivation of a closely related duality relation is presented, which should be understandable to the introductory student.
A textbook interpretation of quantum physics is that quantum objects can be described in a particle or a wave picture, depending on the operations and measurements performed. Beyond this widely held believe, we demonstrate in this contribution that neither the wave nor the particle description is sufficient to predict the outcomes of quantum-optical experiments. To show this, we derive correlation-based criteria that have to be satisfied when either particles or waves are fed into our interferometer. Using squeezed light, it is then confirmed that measured correlations are incompatible with either picture. Thus, within one single experiment, it is proven that neither a wave nor a particle model explains the observed phenomena. Moreover, we formulate a relation of wave and particle representations to two incompatible notions of quantum coherence, a recently discovered resource for quantum information processing.For such an information-theoretic interpretation of our method, we certify the nonclassicality of coherent states - the quantum counterpart to classical waves - in the particle picture, complementing the known fact that photon states are nonclassical in the typically applied wave picture.
A world-wide COVID-19 pandemic intensified strongly the studies of molecular mechanisms related to the coronaviruses. The origin of coronaviruses and the risks of human-to-human, animal-to-human, and human-to-animal transmission of coronaviral infections can be understood only on a broader evolutionary level by detailed comparative studies. In this paper, we studied ribonucleocapsid assembly-packaging signals (RNAPS) in the genomes of all seven known pathogenic human coronaviruses, SARS-CoV, SARS-CoV-2, MERS-CoV, HCoV-OC43, HCoV-HKU1, HCoV-229E, and HCoV-NL63 and compared them with RNAPS in the genomes of the related animal coronaviruses including SARS-Bat-CoV, MERS-Camel-CoV, MHV, Bat-CoV MOP1, TGEV, and one of camel alphacoronaviruses. RNAPS in the genomes of coronaviruses were evolved due to weakly specific interactions between genomic RNA and N proteins in helical nucleocapsids. Combining transitional genome mapping and Jaccard correlation coefficients allows us to perform the analysis directly in terms of underlying motifs distributed over the genome. In all coronaviruses RNAPS were distributed quasi-periodically over the genome with the period about 54 nt biased to 57 nt and to 51 nt for the genomes longer and shorter than that of SARS-CoV, respectively. The comparison with the experimentally verified packaging signals for MERS-CoV, MHV, and TGEV proved that the distribution of particular motifs is strongly correlated with the packaging signals. We also found that many motifs were highly conserved in both characters and positioning on the genomes throughout the lineages that make them promising therapeutic targets. The mechanisms of encapsidation can affect the recombination and co-infection as well.
CoV2019 has evolved to be much more dangerous than CoV2003. Experiments suggest that structural rearrangements dramatically enhance CoV2019 activity. We identify a new first stage of infection which precedes structural rearrangements by using biomolecular evolutionary theory to identify sequence differences enhancing viral attachment rates. We find a small cluster of mutations which show that CoV-2 has a new feature that promotes much stronger viral attachment and enhances contagiousness. The extremely dangerous dynamics of human coronavirus infection is a dramatic example of evolutionary approach of self-organized networks to criticality. It may favor a very successful vaccine. The identified mutations can be used to test the present theory experimentally.
The post-genomic era has brought opportunities to bridge traditionally separate fields of early history of life and brought new insight into origin and evolution of biodiversity. According to distributions of codons in genome sequences, I found a relationship between the genetic code and the tree of life. This remote and profound relationship involves the origin and evolution of the genetic code and the diversification and expansion of genomes. Here, a prebiotic picture of the triplex nucleic acid evolution is proposed to explain the origin of the genetic code, where the transition from disorder to order in the origin of life might be due to the increasing stabilities of triplex base pairs. The codon degeneracy can be obtained in detail based on the coevolution of the genetic code with amino acids, or equivalently, the coevolution of tRNAs with aaRSs. This theory is based on experimental data such as the stability of triplex base pairs and the statistical features of genomic codon distributions. Several experimentally testable proposals have been developed. This study should be regarded as an exploratory attempt to reveal the early evolution of life based on sequence information in a statistical manner.
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