Fate of Neuraminidases of Influenza A Viruses

The current COVID-19 pandemic creates the biggest health and economic challenges to the world. However, not much knowledge is available about this coronavirus, SARS-CoV-2, because of its novelty. Indeed, it necessarily knows the fate of proteins generated by SARS-CoV-2. Anyway, before a large-scale study on proteins from SARS-CoV-2, it would be better to conduct a small-scale study on a well-known protein from influenza A viruses, because both are positive-sense RNA viruses. Thus, we applied a simple method of amino-acid pair probability to analyze 94 neuraminidases of influenza A viruses for better understanding of their fate. The results demonstrate three features of these neuraminidases: (i) the N1 neuraminidases are more susceptible to mutations, which is the current state of the neuraminidases; (ii) the N1 neuraminidases have undergone more mutations in the past, which is the history of the neuraminidases; and (iii) the N1 neuraminidases have a larger potential towards future mutations, which is the future of the neuraminidases. Moreover, our study reveals two clues on the mutation tendency, i.e. the mutations represent a degeneration process, and chickens, ducks and geese are rendered more susceptive to mutation. We hope to apply this approach to study the proteins from SARS-CoV-2 in near future.

Continuous Displacement of “Lattice” Atoms

In the existing CVM (Cluster Variation Method) formulations, atoms are placed on lattice points. A modification is proposed in which an atom can be displaced from a lattice point. The displaced position is written by a vector r, which varies continuously. This model is treated in the CVM framework by regarding an atom at r as a species r. The probability of finding an atom displaced at r in dr is written as f(r)dr, and the corresponding pair probability is written as g(r1, r2)dr1dr2. We formulate using the pair approximation of the CVM in the present paper. The interatomic potential is assumed given, for example as the Lennard-Jones form. The entropy is written in terms of f(r) and g(r1, r2) using the CVM formula. The special feature of the present formulation which is different from the prevailing no-displacement cases of the CVM is that rotational symmetry of the lattice is to be satisfied by the f(r) and g(r1, r2) functions. After the general equations are written in the continuum vector form and in the integral equation formulation, an example of a single-component system is solved by changing integrals into summations over finite intervals. Further we construct simulations of displacement patters in such a way that the pattern satisfies the pair probability distribution which has been calculated as the output of the CVM analysis. The simulated pattern shows the wavy behavior of phonons. Future directions are discussed.

Screening in sedimenting suspensions

Caflisch & Luke (1985) showed that, owing to the long range of the hydrodynamie interactions, the variance of the sedimentation velocity in a random suspension with uniform probability for the positions of the particles is divergent in the sense that it grows without bound as the macroscopic linear dimension of the settling vessel is increased. It is shown here, however, that a Debye-like screening of a particle's velocity disturbance, leading to a finite variance, will occur if the pair probability reflects a net deficit of one particle in the vicinity of each particle. The three-particle interactions, which determine the structure of a dilute, monodisperse suspension of spheres, lead to a deficit of neighbouring particles. The magnitude and range of this deficit are shown to be sufficient to lead to a Debye-like screening of the velocity disturbance at a radial distance of order aϕ−1, where a is the particle radius and ϕ their volume fraction. A self-consistent approximation to the screened conditional average velocity field and pair distribution is presented. The screening leads to a variance of the particle velocity and a particle tracer diffusion coefficient that are finite and of order Us2 and Usaϕ−1, respectively, where Vs is the Stokes settling velocity of the particles in unbounded fluid.