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Register a new userSelf-Organized Networks with Long-Range Interactions: Tandem Darwinian Evolution of $alpha$ and $beta$ Tubulin
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J. C. Phillips
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Cytoskeletons are self-organized networks based on polymerized proteins: actin, tubulin, and driven by motor proteins, such as myosin, kinesin and dynein. Their positive Darwinian evolution enables them to approach optimized functionality (self-organized criticality). Our theoretical analysis uses hydropathic waves to identify and contrast the functional differences between the polymerizing $alpha$ and $beta$ tubulin monomers, which are similar in length and secondary structures, as well as having indistinguishable phylogenetic trees. We show how evolution has improved water-driven flexibility especially for $alpha$ tubulin, and thus facilitated heterodimer microtubule assembly, in agreement with recent atomistic simulations and topological models. We conclude that the failure of phylogenetic analysis to identify functionally specific positive Darwinian evolution has been caused by 20th century technical limitations. These are overcome using 21st century quantitative mathematical methods based on thermodynamic scaling and hydropathic modular averaging. Our most surprising result is the identification of large level sets, especially in hydrophobic extrema, with both thermodynamically first- and second-order scaled water waves. Our calculations include explicitly long-range water-protein interactions described by fractals. We also suggest a much-needed corrective for large protein drug development costs.
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Cytoskeletons are self-organized networks based on polymerized proteins: actin, tubulin, and driven by motor proteins, such as myosin, kinesin and dynein. Their positive Darwinian evolution enables them to approach optimized functionality (self-organized criticality). The principal features of the eukaryotic evolution of the cytoskeleton motor protein myosin-1 parallel those of actin and tubulin, but also show striking differences connected to its dynamical function. Optimized (long) hydropathic waves characterize the molecular level Darwinian evolution towards optimized functionality (self-organized criticality). The N-terminal and central domains of myosin-1 have evolved in eukaryotes at different rates, with the central domain hydropathic extrema being optimally active in humans. A test shows that hydropathic scaling can yield accuracies of better than 1% near optimized functionality. Evolution towards synchronized level extrema is connected to a special function of Mys-1 in humans involving Golgi complexes.
What is life. Schrodingers question is discussed here for a specific protein, villin, which builds cells in tissues that detect taste and sound. Villin is represented by a sequence of 827 amino acids bound to a peptide backbone chain. We focus attention on a limited problem, the Darwinian evolution of villin sequences from chickens to humans. This biophysical problem is analyzed using a new physicical method based on thermodynamic domain scaling, a technique that bridges the gap between physical concepts, self-organized criticality, and conventional biostructural practice. It turns out that the evolutionary changes can be explained by Darwinian selection, which is not generally accepted by biologists at the protein level. The presentation is self-contained, and requires no prior experience with proteins at the molecular level.
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 goal of this study is to explore a new self-healing concept in which fungi are used as a self-healing agent to promote calcium mineral precipitation to fill the cracks in concrete. An initial screening of different species of fungi has been conducted. Fungal growth medium was overlaid onto cured concrete plate. Mycelial discs were aseptically deposited at the plate center. The results showed that, due to the dissolving of Ca(OH)2 from concrete, the pH of the growth medium increased from its original value of 6.5 to 13.0. Despite the drastic pH increase, Trichoderma reesei (ATCC13631) spores germinated into hyphal mycelium and grew equally well with or without concrete. X-ray diffraction (XRD) and scanning electron microscope (SEM) confirmed that the crystals precipitated on the fungal hyphae were composed of calcite. These results indicate that T. reesei has great potential to be used in bio-based self-healing concrete for sustainable infrastructure.
We introduce coarse-grained hydrodynamic equations of motion for diffusion-annihilation system with a power-law long-range interaction. By taking into account fluctuations of the conserved order parameter - charge density - we derive an analytically solvable approximation for the nonconserved order parameter - total particle density. Asymptotic solutions are obtained for the case of random Gaussian initial conditions and for system dimensionality $d geq 2$. Large-t, intermediate-t and small-t asymptotics were calculated and compared with existing scaling theories, exact results and simulation data.
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