Heterogeneous versus bulk nucleation of lysozyme crystals

Heterogeneous (on‐glass) protein crystal nucleation was separated from the bulk one in systems of thin protein solution layers, confined between two glass plates of custom made quasi two‐dimensional all‐glass cells, as well as by applying forced protein solution flow. Two commercial samples of hen‐egg‐white lysozyme, Seikagaku and Sigma were used as model proteins. Applying the classical technique of separation in time of nucleation and growth stages with protein solution layers of thickness 0.05 cm we found that the on‐glass crystal nucleation prevailed highly with Seikagaku HEWL, while on the opposite, bulk nucleated crystals represented the main crystal fraction in Sigma solution. Also using 0.05 cm solution layers nucleation rates were measured separately for the on‐glass and bulk protein crystals. The process was investigated by varying solution layer thicknesses as well, from 0.05 down to 0.01, 0.0065 and 0.002 cm. Studying the influence of the forced protein solution flow on HEWL crystal nucleation the classical double‐pulse technique was modified by separating the nucleation and growth stages not only in time, but simultaneously also in place. In this case we found that the ratio of on‐glass formed crystal nuclei to bulk nuclei depended on the flow velocity, but in different manner with Seikagaku HEWL and Sigma HEWL. A plausible explanation of our experimental results is that the bulk crystal nucleation occurs on foreign surfaces as well, e.g. on rests of source biomaterial, which are always present in the protein solutions. Moreover, biomaterial seems to be more active nucleant than glass. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

气流对水面的冲击效果

通过实验研究了在气流冲击下水面的凹陷情况,并通过理论计算予以解释.结果表明凹陷的体积和深度主要与气流速度、玻璃管内径和玻璃管底部到水面上的距离有关的结论.     

Time-dependent and outflow boundary conditions for Dissipative Particle Dynamics

We propose a simple method to impose both no-slip boundary conditions at fluid-wall interfaces and at outflow boundaries in fully developed regions for Dissipative Particle Dynamics (DPD) fluid systems. The procedure to enforce the no-slip condition is based on a velocity-dependent shear force, which is a generalized force to represent the presence of the solid-wall particles and to maintain locally thermodynamic consistency. We show that this method can be implemented in both steady and time-dependent fluid systems and compare the DPD results with the continuum limit (Navier-Stokes) results. We also develop a force-adaptive method to impose the outflow boundary conditions for fully developed flow with unspecified outflow velocity profile or pressure value. We study flows over the backward-facing step and in idealized arterial bifurcations using a combination of the two new boundary methods with different flow rates. Finally, we explore the applicability of the outflow method in time-dependent flow systems. The outflow boundary method works well for systems with Womersley number of O(1), i.e., when the pressure and flowrate at the outflow are approximately in-phase.     

Sub-iteration leads to accuracy and stability enhancements of semi-implicit schemes for the Navier–Stokes equations

We present an iterative semi-implicit scheme for the incompressible Navier–Stokes equations, which is stable at CFL numbers well above the nominal limit. We have implemented this scheme in conjunction with spectral discretizations, which suffer from serious time step limitations at very high resolution. However, the approach we present is general and can be adopted with finite element and finite difference discretizations as well. Specifically, at each time level, the nonlinear convective term and the pressure boundary condition – both of which are treated explicitly in time – are updated using fixed-point iteration and Aitken relaxation. Eigenvalue analysis shows that this scheme is unconditionally stable for Stokes flows while numerical results suggest that the same is true for steady Navier–Stokes flows as well. This finding is also supported by error analysis that leads to the proper value of the relaxation parameter as a function of the flow parameters. In unsteady flows, second- and third-order temporal accuracy is obtained for the velocity field at CFL number 5–14 using analytical solutions. Systematic accuracy, stability, and cost comparisons are presented against the standard semi-implicit method and a recently proposed fully-implicit scheme that does not require Newton’s iterations. In addition to its enhanced accuracy and stability, the proposed method requires the solution of symmetric only linear systems for which very effective preconditioners exist unlike the fully-implicit schemes.     

Anti-diffusion method for interface steepening in two-phase incompressible flow

In this paper, we present a method for obtaining sharp interfaces in two-phase incompressible flows by an anti-diffusion correction, that is applicable in a straight-forward fashion for the improvement of two-phase flow solution schemes typically employed in practical applications. The underlying discretization is based on the volume-of-fluid (VOF) interface-capturing method on unstructured meshes. The key idea is to steepen the interface, independently of the underlying volume-fraction transport equation, by solving a diffusion equation with reverse time, i.e. an anti-diffusion equation, after each advection time step of the volume fraction. As the solution of the anti-diffusion equation requires regularization, a limiter based on the directional derivative is developed for calculating the gradient of the volume fraction. This limiter ensures the boundedness of the volume fraction. In order to control the amount of anti-diffusion introduced by the correction algorithm we propose a suitable stopping criterion for interface steepening. The formulation of the limiter and the algorithm for solving the anti-diffusion equation are applicable to 3-dimensional unstructured meshes. Validation computations are performed for passive advection of an interface, for 2-dimensional and 3-dimensional rising-bubbles, and for a rising drop in a periodically constricted channel. The results demonstrate that sharp interfaces can be recovered reliably. They show that the accuracy is similar to or even better than that of level-set methods using comparable discretizations for the flow and the level-set evolution. Also, we observe a good agreement with experimental results for the rising drop where proper interface evolution requires accurate mass conservation.     

Energy law preserving C finite element schemes for phase field models in two-phase flow computations

We use the idea in [33] to develop the energy law preserving method and compute the diffusive interface (phase-field) models of Allen–Cahn and Cahn–Hilliard type, respectively, governing the motion of two-phase incompressible flows. We discretize these two models using a C⁰ finite element in space and a modified midpoint scheme in time. To increase the stability in the pressure variable we treat the divergence free condition by a penalty formulation, under which the discrete energy law can still be derived for these diffusive interface models. Through an example we demonstrate that the energy law preserving method is beneficial for computing these multi-phase flow models. We also demonstrate that when applying the energy law preserving method to the model of Cahn–Hilliard type, un-physical interfacial oscillations may occur. We examine the source of such oscillations and a remedy is presented to eliminate the oscillations. A few two-phase incompressible flow examples are computed to show the good performance of our method.     

First-order system least squares and the energetic variational approach for two-phase flow

This paper develops a first-order system least-squares (FOSLS) formulation for equations of two-phase flow. The main goal is to show that this discretization, along with numerical techniques such as nested iteration, algebraic multigrid, and adaptive local refinement, can be used to solve these types of complex fluid flow problems. In addition, from an energetic variational approach, it can be shown that an important quantity to preserve in a given simulation is the energy law. We discuss the energy law and inherent structure for two-phase flow using the Allen–Cahn interface model and indicate how it is related to other complex fluid models, such as magnetohydrodynamics. Finally, we show that, using the FOSLS framework, one can still satisfy the appropriate energy law globally while using well-known numerical techniques.     

Controlling of symmetric and asymmetric mode coupling in long-period fiber gratings singe-side induced by long-pulse CO2 laser

We report a simple fabricating approach to control the mode couplings in long-period fiber gratings (LPFGs) through side exposing fiber to long-pulse-10.6-μm laser from a cheap, internally modulated CO₂ tube. By tuning focused-spot size on fibers, not only circularly symmetric mode coupling but also asymmetric mode couplings can be effectively achieved. Simulation of mode profiles in grating cross-section with Finite Element Method (FEM), and LPFG-cladding etching experiment with hydrofluoric acid (HF), support our explanation that asymmetric mode coupling in LPFGs depends on local refractive-index (RI) change within an azimuthally thin cladding layer, resulted from large-spot method induced deep melt flow on fiber surface during CO₂ laser irradiation.     

壁面结构对非定常薄膜流动表面波特性的影响

采用VOF方法,在入口处引入周期扰动,对沿矩形结构底板下落的二维非定常薄膜流动进行直接数值模拟.计算结果表明,不同频率的外加周期扰动在流场中激发出不同波长的自由表面波.当壁面结构的波长与之相比较小时,由于壁面结构引起的静态波骑行在外加扰动形成的行进波上.若这两个波长相近,非线性效应将促进附近的表面波之间的合并.当薄膜无...     

一阶速度-应力Biot双相各向同性介质弹性波

提出一种等价的一阶双曲型速度一应力Biot双相各向同性介质弹性波波动方程,以实现双相介质混合波场中纯快慢纵波和纯横波波场分离的问题.应用散度和旋度理论证明双相介质等价方程波场分离的可行性,采用高阶交错网格有限差分法构建高精度正演算子,推导其PML吸收边界条件和稳定性条件,并对均匀双相介质和层状非均匀双相介质模型进行数值...