The conformational (structural) change of proteins plays an essential role in their functions. Experiments have been conducted to try to understand the conformational change of proteins, but they have not been successful in providing information on the atomic scale. Simulation methods have been developed to understand the conformational change at an atomic scale in detail. Coarse-grained methods have been developed to calculate protein dynamics with computational efficiency when compared with than all-atom models. A structure-based mass-spring model called the elastic network model (ENM) showed excellent performance in various protein studies. Coarse-grained ENM was modified in various ways to improve the computational efficiency, and consequently to reduce required computational cost for studying the large-scale protein structures. Our previous studies report a modified mass-spring model, which was developed based on condensation method applicable to ENM, and show that the model is able to accurately predict the fluctuation behavior of proteins. We applied this modified mass-spring model to analyze the conformational changes in proteins. We consider two model proteins as an example, where these two proteins exhibit different functions and molecular sizes. It is shown that the modified mass-spring model allows for accurately predicting the pathways of conformation changes for proteins. Our model provides structural insights into the conformation change of proteins related to the biological functions of large protein complexes.

The high speed milling represents the most important process to produce parts in different fields such as aeronautics, automotive and mould. It allows obtaining parts with complex form and with the best surface quality. So, it remains essential to understand the impact of both the cutting force model and its parameters on the tool tip response. Consequently, the mastering of chatter vibration in milling and surface properties of the work piece is essential. In this paper, the simulation of machining is applied to determine the cutting forces distribution. A spindle system modeling is presented using a new approach: Both rigid and flexible modes of the spindle's shaft are taken into account. The shaft is discretized with the Timoshenko beam finite elements with different circular sections. Nonlinear electromagnetic loads exerted by AMBs are computed in terms of the nominal air gap between bearings and spindle, the control current and the displacement of each node. A parametric study is performed to determine the influence of some parameters, such as the feed rate, the tangential cutting coefficient, the spindle speed and the axial depth of the cut on the cutting forces and the chatter vibrations in milling.

In the present study, an exact solution for free vibration analysis of piezoelectric nanobeams based on the nonlocal theory is obtained. The Euler beam model for a long and thin beam structure is employed, together with the electric potential satisfying the surface free charge condition for free vibration analysis. The governing equations and the boundary conditions are derived using Hamilton's principle. These equations are solved analytically for the vibration frequencies of beams with various end conditions. The model has been verified with the previously published works and found a good agreement with them. A detailed parametric study is conducted to discuss the influences of the nonlocal parameter, on the vibration characteristics of piezoelectric nanobeams. The exact vibration solutions should serve as benchmark results for verifying numerically obtained solutions based on other beam models and solution techniques.

On the basis of the linear magnetoelectroelasticity, the interaction problem between a generalized screw dislocation and a fibrous three-phase magnetoelectroelastic composite penetrated by a semi-infinite wedge crack is investigated in this paper. The fibrous magnetoelectroelastic composite is composed of three dissimilar materials bonded along two concentric circular interfaces. The magnetoelectroelastic materials are assumed to be transversely isotropic and have the same poling direction. The analytical derivations are based on the complex variable, conformal mapping, analytical continuation and image singularity methods. Numerical calculations are given graphically for studying the effects of material combinations, geometric models, wedge angles and the load type on the generalized stress fields, the generalized stress intensity factors, and the forces on the dislocation.

This paper presents a 2D dynamics infinite element method (DIEM) for modeling the multiple-hole membrane for vibration analysis. A new concept involving converting the DIEM into a super element that can adjust the hole size and free and fixed boundary conditions around the hole is also proposed. The special element, embedded with an elastic membrane, is formulated on the basis of the conventional finite element method (FEM) by using the similarity mass/stiffness property of isoparametric elements and Craig-Bampton matrix reduction procedures. A DIEM-FE coupling scheme is also developed and self-programmed into the software MATLAB to conduct the vibration analysis of a membrane with multiple holes. The DIEM-FE approach is validated to study the vibration of the rectangular membranes by using the corresponding analytical solutions and the solutions obtained using the conventional FEM. The DIEM-FE is then applied to analyze imbedded L-shaped and circular opening problems. The effects of varying hole diameters and the free or fixed boundary condition along the hole are also examined. Finally, the last example shows that to perform vibration analysis of the multiple-hole membrane, only one DIEM mass/stiffness matrix must be calculated for all holes with an identical circular shape. Overall, this study provides a flexibility and efficient scheme for analyzing a wide variety of membrane vibration problems. The number of degrees of freedom and the corresponding PC memory storage are substantially reduced through the computation.

In this article, a numerical study is carried out for the steady two-dimensional flow of an incompressible Maxwell fluid in the region of oblique stagnation point over a stretching sheet. The governing equations are transformed to dimensionless boundary layer equations. After some manipulation a system of ordinary differential equations is obtained, which is solved by using parallel shooting method. A comparison with the previous studies is made to show the accuracy of our results. The effects of involving parameters are discussed in detail and the streamlines are drawn to predict the flow pattern of the fluid. It is observed that increasing velocities ratio parameter (ratio of straining to stretching velocity) helps to decrease the boundary layer thickness. Furthermore, the velocity of fluid increases by increasing the obliqueness parameter.

The issue on the muzzle blast flow with gas-particle mixtures was numerically investigated in this paper. The propellant gas in the cannon was assumed to be gas-particle mixtures consisting of a variety of gaseous species and particles. The model made use of the Eulerian-Eulerican approach, where the particle were modeled as a second fluid with parameters like bulk density, velocity and temperature, interacting with the gas flow. A high-resolution upwind scheme(AUSMPW+) and detailed reaction kinetics model were employed to solve the chemical non-equilibrium Euler equations for gas phase. The Euler equations for particle phase were solved by MacCormack scheme. The particle diameter and the mass fraction of particle were tested to show their effects on the development process of muzzle blast flow with gas-particle mixtures. The distribution of the main flow parameters of both gas and particle were obtained at different time intervals. The results show the evolution of the muzzle blast flow with gas-particle mixtures and demonstrate the effects of key parameter on the flow field of the gas-particle flow. This paper is a significant investigation for understanding the muzzle blast flow with gas-particle mixtures, which can provide valuable reference for the research on the muzzle blast flow.

The unsteady magnetohydrodynamic free convective flow due to an oscillating porous flat plate in a rotating frame of reference are studied when thermal radiation and Hall currents are taken into consideration. The entire system rotates with a uniform angular velocity about an axis normal to the plate. A uniform magnetic field is applied along the normal to the plate directed into the fluid region. Copper, alumina and titania water nanofluids are considered. The governing equations are solved analytically by employing the small perturbation approximation. The numerical results for fluid velocity and temperature are presented graphically for the pertinent parameters and discussed in details.

Cavitation bubbles, which always exist in the diesel jet leaving the nozzle and in diesel droplets breaking up from the jet as a result of supercavitation of the diesel within the injection nozzle, increase the instability of jet and droplets in part due to the two-phase mixture, while the mechanism of this effect is still unclear. Cavitation bubble expansion within the diesel droplet has been simulated numerically based on the volume of fluid (VOF) method, and the control mechanism of bubble growth process is analyzed by Rayleigh-Plesset equation. The process of bubble growth is divided into three parts, including surface tension controlled domain, comprehensive competition controlled domain and inertial force controlled domain. During the first stage, cavitation bubble growth is controlled by the surface tension, and the decrease of the surface tension leads to the increase of the bubble growth rate. During the second stage, the bubble growth rate is controlled by the comprehensive competition of the surface tension, the inertial force and the viscous force. During the third stage, the process of bubble growth is majorly controlled by the inertial force.

This paper presents experimental results on rapid freezing of water droplets injected into a low temperature environment. A heat balance method was applied to determine the ratio of the water droplets frozen at the collection after the airborne time. The experimental results show that rapid freezing of water droplets could be achieved within three seconds of airborne time. Droplet size distribution of the frozen water droplets after collection was estimated. Heat transfer during the airborne time was calculated with consideration of the droplet size distribution. At attempt was taken to compare the heat transfer obtained with some previous studies on heat transfer of spherical objects in air. The research results show that droplet size distribution is important for the prediction of heat transfer of water droplets traveling in air. The results presented in this study contribute to the understanding of heat transfer of water droplets injected into a low temperature air.

In this paper, the dynamic stall of S809 airfoil that widely used in horizontal axis wind turbine, in different reduced frequencies is investigated. The simulation was carried out numerically handling Navier-Stokes equations. For this purpose, the segregated solver with SIMPLE algorithm was chosen to solve the momentum equations. The effect of turbulence on the flow field is taken into account using Shear Stress Transport (SST) K-ω turbulence model. The obtained numerical results are compared with experimental and a few numerical results. The results indicate that the K-ω SST model is in good agreement with experimental results for both steady and unsteady conditions. Furthermore, a non-dimensional parameter, relating the acceleration of unsteady free stream velocity and acceleration of pitch motion (known as reduced frequency), is also investigated. In addition, the results show that any increase in the reduced frequency increases the instantaneous aerodynamic characteristics of oscillating airfoil.

Simulation of the 3-D, fully developed turbulent channel flows laden with various mass loading ratios of particles is made using an Eulerian-Lagrangian approach in which the carrier-fluid flow field is solved with a low-Reynolds-number k-ε turbulence model while the deterministic Lagrangian method together with binary-collision hard-sphere model is applied for the solution of particle motion. Effects of inter-particle collisions and particle-wall collisions under different extents of wall roughness on particle dispersion are addressed in the study. A cost-effective searching algorithm of collision pair among particles is developed. It is found that the effects of inter-particle collisions on particle dispersion cannot be negligible when the ratio of the mean free time of particle to the mean particle relaxation time of particle is less or equal to O(10). In addition, the wall roughness extent plays an important role in the simulation of particle-wall collisions particularly for cases with small mass loading ratios.