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The Richtmyer–Meshkov and the Rayleigh–Taylor instabilities of viscoplastic (or the Bingham) fluids are studied in the three–dimensional formulation of the problem. A numerical modeling of the intermixing of two fluids with different rheology, whose densities differ twice, as a result of instabilities development process has been carried out. The development of the Richtmyer–Meshkov and the Rayleigh–Taylor instabilities of the Bingham fluids is analyzed utilizing the MacCormack and the Volume of Fluid (VOF) methods to reconstruct the interface during the process. Both the results of numerical simulation of the named instabilities of the Bingham liquids and their comparison with theory and the results of the Newtonian fluid simulation are presented. Critical amplitude of the initial perturbation of the contact boundary velocity field at which the development of instabilities begins was estimated. This critical amplitude presents because of the yield stress exists in the Bingham fluids. Results of numerical calculations show that the yield stress of viscoplastic fluids essentially affects the nature of the development of both Rayleigh–Taylor and Richtmyer–Meshkov instabilities. If the amplitude of the initial perturbation is less than the critical value, then the perturbation decays relatively quickly, and no instability develops.When the initial perturbation exceeds the critical amplitude, the nature of the instability development resembles that of the Newtonian fluid. In a case of the Richtmyer–Meshkov instability, the critical amplitudes of the initial perturbation of the contact boundary at different values of the yield stress are estimated. There is a distinction in behavior of the non-Newtonian fluid in a plane case: with the same value of the yield stress in three-dimensional geometry, the range of the amplitude values of the initial perturbation, when fluid starts to transit from rest to motion, is significantly narrower. In addition, it is shown that the critical amplitude of the initial perturbation of the contact boundary for the Rayleigh–Taylor instability is lower than for the Richtmyer–Meshkov instability. This is due to the action of gravity, which helps the instability to develop and counteracts the forces of viscous friction.

We study the computational properties of a parametric class of finite-volume schemes with customizable dissipative properties with splitting by physical processes into Lagrangian, Eulerian, and the final stages (the hybrid large-particle method). The method has a second-order approximation in space and time on smooth solutions. The regularization of a numerical solution at the Lagrangian stage is performed by nonlinear correction of artificial viscosity. Regardless of the grid resolution, the artificial viscosity value tends to zero outside the zone of discontinuities and extremes in the solution. At Eulerian and final stages, primitive variables (density, velocity, and total energy) are first reconstructed by an additive combination of upwind and central approximations weighted by a flux limiter. Then numerical divergent fluxes are formed from them. In this case, discrete analogs of conservation laws are performed.

The analysis of dissipative properties of the method using known viscosity and flow limiters, as well as their linear combination, is performed. The resolution of the scheme and the quality of numerical solutions are demonstrated by examples of two-dimensional benchmarks: a gas flow around the step with Mach numbers 3, 10 and 20, the double Mach reflection of a strong shock wave, and the implosion problem. The influence of the scheme viscosity of the method on the numerical reproduction of a gases interface instability is studied. It is found that a decrease of the dissipation level in the implosion problem leads to the symmetric solution destruction and formation of a chaotic instability on the contact surface.

Numerical solutions are compared with the results of other authors obtained using higher-order approximation schemes: CABARET, HLLC (Harten Lax van Leer Contact), CFLFh (CFLF hybrid scheme), JT (centered scheme with limiter by Jiang and Tadmor), PPM (Piecewise Parabolic Method), WENO5 (weighted essentially non-oscillatory scheme), RKGD (Runge –Kutta Discontinuous Galerkin), hybrid weighted nonlinear schemes CCSSR-HW4 and CCSSR-HW6. The advantages of the hybrid large-particle method include extended possibilities for solving hyperbolic and mixed types of problems, a good ratio of dissipative and dispersive properties, a combination of algorithmic simplicity and high resolution in problems with complex shock-wave structure, both instability and vortex formation at interfaces.

This work is devoted to the analysis of conformational changes in tubulin dimers and tetramers, in particular, the assessment of the bending of microtubule protofilaments. Three recently exploited approaches for estimating the bend of tubulin protofilaments are reviewed: (1) measurement of the angle between the vector passing through the H7 helices in $\alpha$ and $\beta$ tubulin monomers in the straight structure and the same vector in the curved structure of tubulin; (2) measurement of the angle between the vector, connecting the centers of mass of the subunit and the associated GTP nucleotide, and the vector, connecting the centers of mass of the same nucleotide and the adjacent tubulin subunit; (3) measurement of the three rotation angles of the bent tubulin subunit relative to the straight subunit. Quantitative estimates of the angles calculated at the intra- and inter-dimer interfaces of tubulin in published crystal structures, calculated in accordance with the three metrics, are presented. Intra-dimer angles of tubulin in one structure, measured by the method (3), as well as measurements by this method of the intra-dimer angles in different structures, were more similar, which indicates a lower sensitivity of the method to local changes in tubulin conformation and characterizes the method as more robust. Measuring the angle of curvature between H7-helices (method 1) produces somewhat underestimated values of the curvature per dimer. Method (2), while at first glance generating the bending angle values, consistent the with estimates of curved protofilaments from cryoelectron microscopy, significantly overestimates the angles in the straight structures. For the structures of tubulin tetramers in complex with the stathmin protein, the bending angles calculated with all three metrics varied quite significantly for the first and second dimers (up to 20% or more), which indicates the sensitivity of all metrics to slight variations in the conformation of tubulin dimers within these complexes. A detailed description of the procedures for measuring the bending of tubulin protofilaments, as well as identifying the advantages and disadvantages of various metrics, will increase the reproducibility and clarity of the analysis of tubulin structures in the future, as well as it will hopefully make it easier to compare the results obtained by various scientific groups.