ISPH中的固壁边界的处理

介绍了ISPH(incompressible Smoothed Particle Hydrodynamics,ISPH)的原理,以及SPH的一些基本原理和基本公式后,侧重介绍ISPH的固壁边界的处理方法。通过模拟Couette流,并与WCSPH(Weakly Compressible SPH)的结果及级数解作对比,验证了这种处理方法的有效性。

用ISPH模拟不可压缩流体

介绍了ISPH(incompressible Smoothed Particle Hydrodynamics,ISPH)的原理,以及SPH的一些基本原理和基本公式,分别用ISPH和WCSPH(Weakly Compressible SPH)模拟了不可压缩流体的Poiseuille流。通过与WC-SPH的结果及级数解作对比,验证了ISPH的可行性及其优点。

CS-ISPH-TPP亚微米颗粒的粒径与表面电位影响因素研究

以带正电的几丁聚醣（CS）与带负电的三聚磷酸钠（TPP）通过离子交联作用包覆分离大豆蛋白质水解物（ISPH）制成CS—ISPH—TPP亚微米颗粒，利用动态光散射法分析ISPH浓度、CS分子量及CS／TPP质量比对亚微米颗粒的粒径与表面电位的影响。结果表明，CS-ISPH-TPP亚微米颗粒的粒径随ISPH添加浓度的增加而增大，而表面电位则无明显变化。CS—TPP与CS-ISPH—TPP亚微米颗粒的粒径会随CS分子量的增加而增大，且包覆ISPH颗粒的粒径均大于未包覆的颗粒，而表面电位则介于41．9～44．2mV之间。CS／TPP质量比由6：1减至4：1时，颗粒粒径会随之增加，而由4：1减至2：1时，粒径则变小；CS／TPP质量比由6：1减至3：1时，颗粒表面均带有高度的正电荷，继续减至2：1时，表面电位会出现骤降的情形。

两种边界条件设置方法在ISPH中的比较

以平板驱动二维腔剪切流作为标准算例,对比考察镜像虚粒子与静态虚粒子两种边界设置方法,分别在两种不可压缩流SPH(ISPH-DF与ISPH-DI)中的应用。结果显示,采用静态虚粒子边界,计算精度更高;ISPH-DF算法较ISPH-DI法更加稳定。

模拟自由表面流的新ISPH模型

为了寻求更有效的求解不可压缩流体压力的方法,本文基于SHAKE方法构建了一种新的能够模拟宏观自由表面流的ISPH模型。在该模型中,控制方程采用不可压缩Navier-Stokes方程和k-ε湍流方程。在采用SPH表达式和二阶Runge-Kutta时间积分算子对控制方程进行空-时离散的基础上,以水流粒子始终保持初始体积作为约束条件,利用SHAKE方法显式地迭代求解压力项,构建了能够模拟宏观自由表面流的ISPH模型。基于典型溃坝算例,系统比较分析了本文基于SHAKE法的ISPH模型、基于投影法的ISPH模型和VOF模型的模拟效果。结果表明,基于SHAKE法和基于投影法的ISPH模型均能模拟溃坝过程中自由表面水流溅落及水波相撞等大变形物理细节过程,且模拟结果基本相同。与之相比,VOF模型难以模拟该类大变形物理过程,但能够模拟出溃坝过程的主要特征,且水压力分布更趋光滑。与基于投影法的ISPH模型相比,基于SHAKE法的ISPH模型能够完全阻止光滑粒子的非物理穿透现象,数值模拟过程中无任何质量损失。

金银花类药用植物IspE和IspH基因克隆和生物信息学分析

目的:克隆金银花类药用植物4-二磷酸胞苷-2-C-甲基赤藓糖激酶(4-diphosphocytidyl-2-C-methyl-D-erythritol ki-nase,IspE)和4-羟基-3-甲基-2-邻苯基二磷酸还原酶(4-hydroxy-3-methylbut-2-enyl diphosphate reductase,IspH)基因,并对其基因序列、蛋白特性和转录活性进行分析、比较。方法:从忍冬Lonicera japonica转录组测序结果中分析获得了IspE,IspH基因。分别以忍冬、红白忍冬L.japonica var.chinensis、红腺忍冬L.hypoglauca和水忍冬L.dasystyla新鲜花蕾为材料,利用RT-PCR技术克隆获得了4种金银花类药用植物IspE和IspH基因的全长cDNA。运用生物信息学分析软件,预测编码蛋白的结构和功能,并通过RT-PCR检测IspE和IspH在忍冬、红白忍冬、红腺忍冬、水忍冬花蕾中的转录情况。结果:金银花类药用植物IspE基因含有1个完整的开放阅读框,长度为1 221 bp,编码406个氨基酸;IspH含有一个完整的开放阅读框,长度为1 380 bp,编码459个氨基酸。IspE和IspH均为非分泌蛋白,均定位于叶绿体中。RT-PCR分析结果表明在忍冬、红腺忍冬和水忍冬的花蕾中IspE,IspH基因的转录水平没有显著差异,但红白忍冬花蕾中IspE,IspH基因的转录水平均显著高于忍冬。结论:克隆获得忍冬、红白忍冬、红腺忍冬和水忍冬中IspE,IspH基因,并证实了其在不同金银花类药用植物中的表达,为进一步研究IspE,IspH基因对萜类化合物生物合成和花香气以及颜色的影响奠定了基础。

Water entry of decelerating spheres simulations using improved ISPH method

In this paper, we simulated the vertical impact of spheres on a water surface using three-dimensional incompressible smoothed particle hydrodynamics(3-D ISPH) method. The sphere motion is taken to be a rigid body motion and it is modeled by ISPH method. The governing equations are discretized and solved numerically using ISPH method. A stabilized incompressible SPH method by relaxing the density invariance condition is adopted. Here, we computed the motions of a rigid body by direct integration of the fluid pressure at the position of each particle on the body surface. The equations of translational and rotational motion were integrated in time domain to update the position of the rigid body at each time step. In this study, we improved the boundary treatment between fluid and fixed solid boundary by using virtual marker technique. In addition, an improved algorithm based on the virtual marker technique for the boundary particles is proposed to treat the moving boundary of the rigid body motion. The force exerted on the moving rigid boundary particles by the surrounding particles, is calculated by the SPH approximation at the virtual marker points. The applicability and efficiency of the current ISPH method are tested by comparison with reference experimental results.

烟草IspH基因的克隆与原核表达

IspH基因作为MEP途径中的关键酶具有促进下游萜类化合物产量的积累和提高植物对外界的抵御能力的特定作用,本研究旨在通过对烟草中IspH基因进行克隆与原核表达分析,从野生型烟草中提取总RNA,通过RT-PCR克隆获得IspH基因的cDNA序列(NCBI登录号:KC480443),序列分析表明,IspH基因的开放阅读框(ORF)长为1386 bp,编码461个氨基酸,其编码的蛋白具有LytB个高度保守结构域;通过构建pET28a-IspH原核表达载体,转化到Escherichia coli BL21(DE3)中,经IPTG诱导、SDS-PAGE电泳和Western Blot检测IspH蛋白,与预期大小一致约为51 kD,浓度为0.410 mg/mL,且纯度达到90%以上。目的蛋白的成功表达为进一步研究IspH基因在植物发育和抗逆性中的功能研究提供理论参考和数据支持。

Simulation of Wave Impact on a Horizontal Deck Based on SPH Method

A numerical model was established for simulating wave impact on a horizontal deck by an improved incompressible smoothed particle hydrodynamics (ISPH). As a grid-less particle method, the ISPH method has been widely used in the free-surface hydrodynamic flows with good accuracy. The improvement includes the employment of a corrective function for enhancement of angular momentum conservation in a particle-based calculation and a new estimation method to predict the pressure on the horizontal deck. The simulation results show a good agreement with the experiment. The present numerical model can be used to study wave impact load on the horizontal deck.

Simulation of Wave Impact on Three-Dimensional Horizontal Plate Based on SPH Method

An improved three-dimensional incompressible smooth particle hydrodynamics(ISPH)model is developed to simulate the impact of regular wave on a horizontal plate.The improvement is the employment of a corrective function to enhance angular momentum conservation in a particle-based calculation.And a new estimation method is proposed to predict the pressure on the horizontal plate.Then,the model simulates the variation characteristics of impact pressures generated by regular wave slamming.The main features of velocity field and pressure field near the plate are presented.The present numerical model can be used to study wave impact load on the horizontal plate.

Comparative Study of Different SPH Schemes on Simulating Violent Water Wave Impact Flows

Free surface flows are of significant interest in Computational Fluid Dynamics（CFD）. However, violent water wave impact simulation especially when free surface breaks or impacts on solid wall can be a big challenge for many CFD techniques. Smoothed Particle Hydrodynamics（SPH） has been reported as a robust and reliable method for simulating violent free surface flows. Weakly compressible SPH（WCSPH） uses an equation of state with a large sound speed, and the results of the WCSPH can induce a noisy pressure field and spurious oscillation of pressure in time history for wave impact problem simulation. As a remedy, the truly incompressible SPH（ISPH） technique was introduced, which uses a pressure Poisson equation to calculate the pressure. Although the pressure distribution in the whole field obtained by ISPH is smooth, the stability of the techniques is still an open discussion. In this paper, a new free surface identification scheme and solid boundary handling method are introduced to improve the accuracy of ISPH. This modified ISPH is used to study dam breaking flow and violent tank sloshing flows. On the comparative study of WCSPH and ISPH, the accuracy and efficiency are assessed and the results are compared with the experimental data.

Natural Convection in an H-Shaped Porous EnclosureFilled with a Nanofluid

This study simulates natural convection flow resulting from heat partitions in an H-shaped enclosure filled with a nanofluid using an incompressible smoothed particle hydrodynamics(ISPH)method.The right area of the H-shaped enclosure is saturated with non-Darcy porous media.The center variable partitions of the H-shaped enclosure walls are kept at a high-temperature Th.The left and right walls of the H-shaped enclosure are positioned at a low temperature Tc and the other walls are adiabatic.In ISPH method,the source term in pressure Poisson equation(PPE)is modified.The influences of the controlling parameters on the temperature distributions,the velocity field and average Nusselt number are discussed.The performed simulations proofed that the length of the heated partitions augments the velocity field and temperature distributions in an H-shaped enclosure.Rayleigh number rises the fluid velocity and heat transfer in an H-shaped enclosure.The porous layer on the right side of the H-shaped enclosure at a lower Darcy parameter causes a high resistance force for the fluid flow and heat transfer characteristic inside an H-shaped enclosure.Added nanoparticles reduces the velocity field and enhances the heat transfer inside an H-shaped enclosure.

Simulation of Water-Soil-Structure Interactions Using Incompressible Smoothed Particle Hydrodynamics

In the present work,an incompressible smoothed particle hydrodynamic(SPH)method is introduced to simulate water-soil-structure interactions.In the current calculation,the water is modelled as a Newtonian fluid.The soil is modelled in two different cases.In the first case,the granular material is considered as a fluid where a Bingham type constitutive model is proposed based on Mohr-Coulomb yield-stress criterion,and the viscosity is derived from the cohesion and friction angle.In addition,the fictitious suspension layers between water and soil depending on the concentration of soil are introduced.In the second case,Hooke’s law introduces elastic soil.In ISPH,the pressure is evaluated by solving the pressure Poisson equation using a semi-implicit algorithm based on the projection method and an eddy viscosity for water is modelled by a large eddy simulation with the Smagorinsky model.In the proposed ISPH method,the pressure is stabilized to simulate the multiphase flow between soil and water.Numerical experiments for water-soil suspension flow of Louvain erosional dam break with flat soil foundation,is simulated and validated using 3D-ISPH method.Coupling between water-soil interactions with different solid structures are simulated.The results revealed that,the suspension layers with the Bingham model of soil gives more accurate results in the experiment as compared to the case of the Bingham model without suspension layers.In addition,the elastic soil model by the Hooke’s law can simulate soil hump accurately as compared to the Bingham model.From the simulations,avoiding erosion behind the structure for preventing the structure break during flood are investigated by using an extended structure or a wedge structure.

Map-Based Cloning of zb7 Encoding an IPP and DMAPP Synthase in the MEP Pathway of Maize

IspH is a key enzyme in the last step of the methyI-D-erythritol-4-phosphate （MEP） pathway. Loss of function of IspH can often result in complete yellow or albino phenotype in many plants. Here, we report the characterization of a recessive mutant of maize, zebra7 （zb7）, showing transverse green/yellow striped leaves in young plants. The yellow bands of the mutant have decreased levels of chlorophylls and carotenoids with delayed chloroplast development. Low temperature suppressed mutant phenotype, while alternate light/dark cycle or high temperature enlarged the yellow section. Map-based cloning demonstrated that zb7 encodes the IspH protein with a mis-sense mutation in a conserved region. Transgenic silencing of Zb7 in maize resulted in complete albino plantlets that are aborted in a few weeks, confirming that Zb7 is important in the early stages of maize chloroplast development. Zb7 is constitutively expressed and its expression subject to a 16-h light/8-h dark cycle regulation. Our results suggest that the less effective or unstable IspH in zb7 mutant, together with its diurnal expression, are mechanistically accounted for the zebra phenotype. The increased IspH mRNA in the leaves of zb7 at the late development stage may explain the restoration of mutant phenotype in mature stages.

Towards development of enhanced fully-Lagrangian mesh-free computational methods for fluid-structure interaction

Simulation of incompressible fluid flow-elastic structure interactions is targeted by using fully-Lagrangian mesh-free computational methods. A projection-based fluid model（moving particle semi-implicit（MPS）） is coupled with either a Newtonian or a Hamiltonian Lagrangian structure model（MPS or HMPS） in a mathematically-physically consistent manner. The fluid model is founded on the solution of Navier-Stokes and continuity equations. The structure models are configured either in the framework of Newtonian mechanics on the basis of conservation of linear and angular momenta, or Hamiltonian mechanics on the basis of variational principle for incompressible elastodynamics. A set of enhanced schemes are incorporated for projection-based fluid model（Enhanced MPS）, thus, the developed coupled solvers for fluid structure interaction（FSI） are referred to as Enhanced MPS-MPS and Enhanced MPS-HMPS. Besides, two smoothed particle hydrodynamics（SPH）-based FSI solvers, being developed by the authors, are considered and their potential applicability and comparable performance are briefly discussed in comparison with MPS-based FSI solvers. The SPH-based FSI solvers are established through coupling of projection-based incompressible SPH（ISPH） fluid model and SPH-based Newtonian/Hamiltonian structure models, leading to Enhanced ISPH-SPH and Enhanced ISPH-HSPH. A comparative study is carried out on the performances of the FSI solvers through a set of benchmark tests, including hydrostatic water column on an elastic plate,high speed impact of an elastic aluminum beam, hydroelastic slamming of a marine panel and dam break with elastic gate.

Numerical modeling of sediment transport based on unsteady and steady flows by incompressible smoothed particle hydrodynamics method

The purpose of the present paper is to introduce a simple two-part multi-phase model for the sediment transport problems based on the incompressible smoothed particle hydrodynamics（ISPH） method. The proposed model simulates the movement of sediment particles in two parts. The sediment particles are classified into three categories, including the motionless particles, moving particles behave like a rigid body, and moving particles with a pseudo fluid behavior. The criterion for the classification of sediment particles is the Bingham rheological model. Verification of the present model is performed by simulation of the dam break waves on movable beds with different conditions and the bed scouring under steady flow condition. Comparison of the present model results, the experimental data and available numerical results show that it has good ability to simulate flow pattern and sediment transport.

Incompressible SPH simulation of solitary wave propagation on permeable beaches

Wave propagation on uniformly sloped beaches is a canonical coastal engineering topic that has been studied extensively in the past few decades.However,most of these studies treat beaches as solid boundaries even though they are often made of porous materials,such as sediment and vegetation.Permeable beaches struck by tsunami-like waves have not been adequately investigated.It is expected that the degree of penneability plays a crucial role in mitigating the impact of the wave.This study examines solitary wave run-ups on sandy beaches using an incompressible smoothed particle hydrodynamics(ISPH)model.The permeability of the beach is considered to be directly related to the diameter of its constituent sand particles.To obtain a satisfactory pressure field,which cannot be achieved using the original ISPH algorithm,the source term of the pressure Poisson equation has been modified based on a higher-order source-term expression.Flows within the porous medium are computed in the same framework as those outside the porous medium.In the current model,no transition zone is needed at the boundary of the porous structure.The wave-attenuation effect of the porous medium is discussed,with a particular focus on the relationship between the mn-up height and grainsize.

Magnetic impact on heat and mass transfer utilizing nonofluid in an annulus between a superellipse obstacle and a cavity with periodic side-wall temperature and concentration

The magnetic impacts upon the transport of heat and mass of an electrically conducting nanofluid within an annulus among an inner rhombus with convex and outer cavity with periodic temperature/concentration profiles on its left wall are assessed by the ISPH method.The right wall has Tcand C,cflat walls are adiabatic,and the temperature and concentration of the left wall are altered sinusoidally with time.The features of the heat and mass transfer and fluid flow through an annulus are assessed across a wide scale of Hartmann number Ha,Soret number Sr,oscillation amplitude A,Dufour number Du,nanoparticles parameterΦ,oscillation frequency f,Rayleigh number Ra,and radius of a superellipse a at Lewis number Le=20,magnetic field’s angle g=45°,Prandtl number Pr=6.2,a superellipse coefficient n=3/2,and buoyancy parameter N=1.The results reveal that the velocity’s maximum reduces by 70.93%as Ha boosts from 0 to 50,and by 66.24%as coefficient a boosts from 0.1 to 0.4.Whilst the velocity’s maximum augments by 83.04%as Sr increases from 0.6 to 2 plus a decrease in Du from 1 to0.03.The oscillation amplitude A,and frequency f are significantly affecting the nanofluid speed,and heat and mass transfer inside an annulus.Increasing the parameters A and f is augmenting the values of mean Nusselt number-(Sh)and mean Sherwood number^-(Nu).Increasing the radius of a superellipse a enhances the values of^(Nu)and^(Sh).