Steel Fibre Reinforced Concrete Simulation with the SPH Method

NASA Astrophysics Data System (ADS)

Hušek, Martin; Kala, Jiří; Král, Petr; Hokeš, Filip

2017-10-01

Steel fibre reinforced concrete (SFRC) is very popular in many branches of civil engineering. Thanks to its increased ductility, it is able to resist various types of loading. When designing a structure, the mechanical behaviour of SFRC can be described by currently available material models (with equivalent material for example) and therefore no problems arise with numerical simulations. But in many scenarios, e.g. high speed loading, it would be a mistake to use such an equivalent material. Physical modelling of the steel fibres used in concrete is usually problematic, though. It is necessary to consider the fact that mesh-based methods are very unsuitable for high-speed simulations with regard to the issues that occur due to the effect of excessive mesh deformation. So-called meshfree methods are much more suitable for this purpose. The Smoothed Particle Hydrodynamics (SPH) method is currently the best choice, thanks to its advantages. However, a numerical defect known as tensile instability may appear when the SPH method is used. It causes the development of numerical (false) cracks, making simulations of ductile types of failure significantly more difficult to perform. The contribution therefore deals with the description of a procedure for avoiding this defect and successfully simulating the behaviour of SFRC with the SPH method. The essence of the problem lies in the choice of coordinates and the description of the integration domain derived from them - spatial (Eulerian kernel) or material coordinates (Lagrangian kernel). The contribution describes the behaviour of both formulations. Conclusions are drawn from the fundamental tasks, and the contribution additionally demonstrates the functionality of SFRC simulations. The random generation of steel fibres and their inclusion in simulations are also discussed. The functionality of the method is supported by the results of pressure test simulations which compare various levels of fibre reinforcement of SFRC

Simulations of reactive transport and precipitation with smoothed particle hydrodynamics

NASA Astrophysics Data System (ADS)

Tartakovsky, Alexandre M.; Meakin, Paul; Scheibe, Timothy D.; Eichler West, Rogene M.

2007-03-01

A numerical model based on smoothed particle hydrodynamics (SPH) was developed for reactive transport and mineral precipitation in fractured and porous materials. Because of its Lagrangian particle nature, SPH has several advantages for modeling Navier-Stokes flow and reactive transport including: (1) in a Lagrangian framework there is no non-linear term in the momentum conservation equation, so that accurate solutions can be obtained for momentum dominated flows and; (2) complicated physical and chemical processes such as surface growth due to precipitation/dissolution and chemical reactions are easy to implement. In addition, SPH simulations explicitly conserve mass and linear momentum. The SPH solution of the diffusion equation with fixed and moving reactive solid-fluid boundaries was compared with analytical solutions, Lattice Boltzmann [Q. Kang, D. Zhang, P. Lichtner, I. Tsimpanogiannis, Lattice Boltzmann model for crystal growth from supersaturated solution, Geophysical Research Letters, 31 (2004) L21604] simulations and diffusion limited aggregation (DLA) [P. Meakin, Fractals, scaling and far from equilibrium. Cambridge University Press, Cambridge, UK, 1998] model simulations. To illustrate the capabilities of the model, coupled three-dimensional flow, reactive transport and precipitation in a fracture aperture with a complex geometry were simulated.

X-Ray modeling of η Carinae & WR 140 from SPH simulations

NASA Astrophysics Data System (ADS)

Russell, Christopher M. P.; Corcoran, Michael F.; Okazaki, Atsuo T.; Madura, Thomas I.; Owocki, Stanley P.

2011-07-01

The colliding wind binary (CWB) systems η Carinae and WR140 provide unique laboratories for X-ray astrophysics. Their wind-wind collisions produce hard X-rays that have been monitored extensively by several X-ray telescopes, including RXTE. To interpret these RXTE X-ray light curves, we apply 3D hydrodynamic simulations of the wind-wind collision using smoothed particle hydrodynamics (SPH). We find adiabatic simulations that account for the absorption of X-rays from an assumed point source of X-ray emission at the apex of the wind-collision shock cone can closely match the RXTE light curves of both η Car and WR140. This point-source model can also explain the early recovery of η Car's X-ray light curve from the 2009.0 minimum by a factor of 2-4 reduction in the mass loss rate of η Car. Our more recent models account for the extended emission and absorption along the full wind-wind interaction shock front. For WR140, the computed X-ray light curves again match the RXTE observations quite well. But for η Car, a hot, post-periastron bubble leads to an emission level that does not match the extended X-ray minimum observed by RXTE. Initial results from incorporating radiative cooling and radiative forces via an anti-gravity approach into the SPH code are also discussed.

Spatio-Temporal Process Simulation of Dam-Break Flood Based on SPH

NASA Astrophysics Data System (ADS)

Wang, H.; Ye, F.; Ouyang, S.; Li, Z.

2018-04-01

On the basis of introducing the SPH (Smooth Particle Hydrodynamics) simulation method, the key research problems were given solutions in this paper, which ere the spatial scale and temporal scale adapting to the GIS(Geographical Information System) application, the boundary condition equations combined with the underlying surface, and the kernel function and parameters applicable to dam-break flood simulation. In this regards, a calculation method of spatio-temporal process emulation with elaborate particles for dam-break flood was proposed. Moreover the spatio-temporal process was dynamic simulated by using GIS modelling and visualization. The results show that the method gets more information, objectiveness and real situations.

Smoothed particle hydrodynamics method from a large eddy simulation perspective

NASA Astrophysics Data System (ADS)

Di Mascio, A.; Antuono, M.; Colagrossi, A.; Marrone, S.

2017-03-01

The Smoothed Particle Hydrodynamics (SPH) method, often used for the modelling of the Navier-Stokes equations by a meshless Lagrangian approach, is revisited from the point of view of Large Eddy Simulation (LES). To this aim, the LES filtering procedure is recast in a Lagrangian framework by defining a filter that moves with the positions of the fluid particles at the filtered velocity. It is shown that the SPH smoothing procedure can be reinterpreted as a sort of LES Lagrangian filtering, and that, besides the terms coming from the LES convolution, additional contributions (never accounted for in the SPH literature) appear in the equations when formulated in a filtered fashion. Appropriate closure formulas are derived for the additional terms and a preliminary numerical test is provided to show the main features of the proposed LES-SPH model.

Modelling multi-phase liquid-sediment scour and resuspension induced by rapid flows using Smoothed Particle Hydrodynamics (SPH) accelerated with a Graphics Processing Unit (GPU)

NASA Astrophysics Data System (ADS)

Fourtakas, G.; Rogers, B. D.

2016-06-01

A two-phase numerical model using Smoothed Particle Hydrodynamics (SPH) is applied to two-phase liquid-sediments flows. The absence of a mesh in SPH is ideal for interfacial and highly non-linear flows with changing fragmentation of the interface, mixing and resuspension. The rheology of sediment induced under rapid flows undergoes several states which are only partially described by previous research in SPH. This paper attempts to bridge the gap between the geotechnics, non-Newtonian and Newtonian flows by proposing a model that combines the yielding, shear and suspension layer which are needed to predict accurately the global erosion phenomena, from a hydrodynamics prospective. The numerical SPH scheme is based on the explicit treatment of both phases using Newtonian and the non-Newtonian Bingham-type Herschel-Bulkley-Papanastasiou constitutive model. This is supplemented by the Drucker-Prager yield criterion to predict the onset of yielding of the sediment surface and a concentration suspension model. The multi-phase model has been compared with experimental and 2-D reference numerical models for scour following a dry-bed dam break yielding satisfactory results and improvements over well-known SPH multi-phase models. With 3-D simulations requiring a large number of particles, the code is accelerated with a graphics processing unit (GPU) in the open-source DualSPHysics code. The implementation and optimisation of the code achieved a speed up of x58 over an optimised single thread serial code. A 3-D dam break over a non-cohesive erodible bed simulation with over 4 million particles yields close agreement with experimental scour and water surface profiles.

SPH-based numerical simulations of flow slides in municipal solid waste landfills.

PubMed

Huang, Yu; Dai, Zili; Zhang, Weijie; Huang, Maosong

2013-03-01

Most municipal solid waste (MSW) is disposed of in landfills. Over the past few decades, catastrophic flow slides have occurred in MSW landfills around the world, causing substantial economic damage and occasionally resulting in human victims. It is therefore important to predict the run-out, velocity and depth of such slides in order to provide adequate mitigation and protection measures. To overcome the limitations of traditional numerical methods for modelling flow slides, a mesh-free particle method entitled smoothed particle hydrodynamics (SPH) is introduced in this paper. The Navier-Stokes equations were adopted as the governing equations and a Bingham model was adopted to analyse the relationship between material stress rates and particle motion velocity. The accuracy of the model is assessed using a series of verifications, and then flow slides that occurred in landfills located in Sarajevo and Bandung were simulated to extend its applications. The simulated results match the field data well and highlight the capability of the proposed SPH modelling method to simulate such complex phenomena as flow slides in MSW landfills.

An improved weakly compressible SPH method for simulating free surface flows of viscous and viscoelastic fluids

NASA Astrophysics Data System (ADS)

Xu, Xiaoyang; Deng, Xiao-Long

2016-04-01

In this paper, an improved weakly compressible smoothed particle hydrodynamics (SPH) method is proposed to simulate transient free surface flows of viscous and viscoelastic fluids. The improved SPH algorithm includes the implementation of (i) the mixed symmetric correction of kernel gradient to improve the accuracy and stability of traditional SPH method and (ii) the Rusanov flux in the continuity equation for improving the computation of pressure distributions in the dynamics of liquids. To assess the effectiveness of the improved SPH algorithm, a number of numerical examples including the stretching of an initially circular water drop, dam breaking flow against a vertical wall, the impact of viscous and viscoelastic fluid drop with a rigid wall, and the extrudate swell of viscoelastic fluid have been presented and compared with available numerical and experimental data in literature. The convergent behavior of the improved SPH algorithm has also been studied by using different number of particles. All numerical results demonstrate that the improved SPH algorithm proposed here is capable of modeling free surface flows of viscous and viscoelastic fluids accurately and stably, and even more important, also computing an accurate and little oscillatory pressure field.

RAM simulation model for SPH/RSV systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schryver, J.C.; Primm, A.H.; Nelson, S.C.

1995-12-31

The US Army`s Project Manager, Crusader is sponsoring the development of technologies that apply to the Self-Propelled Howitzer (SPH), formerly the Advanced Field Artillery System (AFAS), and Resupply Vehicle (RSV), formerly the Future Armored Resupply Vehicle (FARV), weapon system. Oak Ridge National Laboratory (ORNL) is currently performing developmental work in support of the SPH/PSV Crusader system. Supportive analyses of reliability, availability, and maintainability (RAM) aspects were also performed for the SPH/RSV effort. During FY 1994 and FY 1995 OPNL conducted a feasibility study to demonstrate the application of simulation modeling for RAM analysis of the Crusader system. Following completion ofmore » the feasibility study, a full-scale RAM simulation model of the Crusader system was developed for both the SPH and PSV. This report provides documentation for the simulation model as well as instructions in the proper execution and utilization of the model for the conduct of RAM analyses.« less

SPH simulation of free surface flow over a sharp-crested weir

NASA Astrophysics Data System (ADS)

Ferrari, Angela

2010-03-01

In this paper the numerical simulation of a free surface flow over a sharp-crested weir is presented. Since in this case the usual shallow water assumptions are not satisfied, we propose to solve the problem using the full weakly compressible Navier-Stokes equations with the Tait equation of state for water. The numerical method used consists of the new meshless Smooth Particle Hydrodynamics (SPH) formulation proposed by Ferrari et al. (2009) [8], that accurately tracks the free surface profile and provides monotone pressure fields. Thus, the unsteady evolution of the complex moving material interface (free surface) can been properly solved. The simulations involving about half a million of fluid particles have been run in parallel on two of the most powerful High Performance Computing (HPC) facilities in Europe. The validation of the results has been carried out analysing the pressure field and comparing the free surface profiles obtained with the SPH scheme with experimental measurements available in literature [18]. A very good quantitative agreement has been obtained.

Numerical Analysis Study of Sarawak Barrage River Bed Erosion and Scouring by Using Smooth Particle Hydrodynamic (SPH)

NASA Astrophysics Data System (ADS)

Zainol, M. R. R. M. A.; Kamaruddin, M. A.; Zawawi, M. H.; Wahab, K. A.

2017-11-01

Smooth Particle Hydrodynamic is the three-dimensional (3D) model. In this research work, three cases and one validation have been simulate using DualSPHysics. Study area of this research work was at Sarawak Barrage. The cases have different water level at the downstream. This study actually to simulate riverbed erosion and scouring properties by using multi-phases cases which use sand as sediment and water. The velocity and the scouring profile have been recorded as the result and shown in the result chapter. The result of the validation is acceptable where the scouring profile and the velocity were slightly different between laboratory experiment and simulation. Hence, it can be concluded that the simulation by using SPH can be used as the alternative to simulate the real cases.

EXAMINING THE ACCURACY OF ASTROPHYSICAL DISK SIMULATIONS WITH A GENERALIZED HYDRODYNAMICAL TEST PROBLEM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Raskin, Cody; Owen, J. Michael, E-mail: raskin1@llnl.gov, E-mail: mikeowen@llnl.gov

2016-11-01

We discuss a generalization of the classic Keplerian disk test problem allowing for both pressure and rotational support, as a method of testing astrophysical codes incorporating both gravitation and hydrodynamics. We argue for the inclusion of pressure in rotating disk simulations on the grounds that realistic, astrophysical disks exhibit non-negligible pressure support. We then apply this test problem to examine the performance of various smoothed particle hydrodynamics (SPH) methods incorporating a number of improvements proposed over the years to address problems noted in modeling the classical gravitation-only Keplerian disk. We also apply this test to a newly developed extension ofmore » SPH based on reproducing kernels called CRKSPH. Counterintuitively, we find that pressure support worsens the performance of traditional SPH on this problem, causing unphysical collapse away from the steady-state disk solution even more rapidly than the purely gravitational problem, whereas CRKSPH greatly reduces this error.« less

SPHYNX: an accurate density-based SPH method for astrophysical applications

NASA Astrophysics Data System (ADS)

Cabezón, R. M.; García-Senz, D.; Figueira, J.

2017-10-01

Aims: Hydrodynamical instabilities and shocks are ubiquitous in astrophysical scenarios. Therefore, an accurate numerical simulation of these phenomena is mandatory to correctly model and understand many astrophysical events, such as supernovas, stellar collisions, or planetary formation. In this work, we attempt to address many of the problems that a commonly used technique, smoothed particle hydrodynamics (SPH), has when dealing with subsonic hydrodynamical instabilities or shocks. To that aim we built a new SPH code named SPHYNX, that includes many of the recent advances in the SPH technique and some other new ones, which we present here. Methods: SPHYNX is of Newtonian type and grounded in the Euler-Lagrange formulation of the smoothed-particle hydrodynamics technique. Its distinctive features are: the use of an integral approach to estimating the gradients; the use of a flexible family of interpolators called sinc kernels, which suppress pairing instability; and the incorporation of a new type of volume element which provides a better partition of the unity. Unlike other modern formulations, which consider volume elements linked to pressure, our volume element choice relies on density. SPHYNX is, therefore, a density-based SPH code. Results: A novel computational hydrodynamic code oriented to Astrophysical applications is described, discussed, and validated in the following pages. The ensuing code conserves mass, linear and angular momentum, energy, entropy, and preserves kernel normalization even in strong shocks. In our proposal, the estimation of gradients is enhanced using an integral approach. Additionally, we introduce a new family of volume elements which reduce the so-called tensile instability. Both features help to suppress the damp which often prevents the growth of hydrodynamic instabilities in regular SPH codes. Conclusions: On the whole, SPHYNX has passed the verification tests described below. For identical particle setting and initial

Incompressible SPH method for simulating Newtonian and non-Newtonian flows with a free surface

NASA Astrophysics Data System (ADS)

Shao, Songdong; Lo, Edmond Y. M.

An incompressible smoothed particle hydrodynamics (SPH) method is presented to simulate Newtonian and non-Newtonian flows with free surfaces. The basic equations solved are the incompressible mass conservation and Navier-Stokes equations. The method uses prediction-correction fractional steps with the temporal velocity field integrated forward in time without enforcing incompressibility in the prediction step. The resulting deviation of particle density is then implicitly projected onto a divergence-free space to satisfy incompressibility through a pressure Poisson equation derived from an approximate pressure projection. Various SPH formulations are employed in the discretization of the relevant gradient, divergence and Laplacian terms. Free surfaces are identified by the particles whose density is below a set point. Wall boundaries are represented by particles whose positions are fixed. The SPH formulation is also extended to non-Newtonian flows and demonstrated using the Cross rheological model. The incompressible SPH method is tested by typical 2-D dam-break problems in which both water and fluid mud are considered. The computations are in good agreement with available experimental data. The different flow features between Newtonian and non-Newtonian flows after the dam-break are discussed.

A density-adaptive SPH method with kernel gradient correction for modeling explosive welding

NASA Astrophysics Data System (ADS)

Liu, M. B.; Zhang, Z. L.; Feng, D. L.

2017-09-01

Explosive welding involves processes like the detonation of explosive, impact of metal structures and strong fluid-structure interaction, while the whole process of explosive welding has not been well modeled before. In this paper, a novel smoothed particle hydrodynamics (SPH) model is developed to simulate explosive welding. In the SPH model, a kernel gradient correction algorithm is used to achieve better computational accuracy. A density adapting technique which can effectively treat large density ratio is also proposed. The developed SPH model is firstly validated by simulating a benchmark problem of one-dimensional TNT detonation and an impact welding problem. The SPH model is then successfully applied to simulate the whole process of explosive welding. It is demonstrated that the presented SPH method can capture typical physics in explosive welding including explosion wave, welding surface morphology, jet flow and acceleration of the flyer plate. The welding angle obtained from the SPH simulation agrees well with that from a kinematic analysis.

Smoothed Particle Hydrodynamics Simulations of Ultrarelativistic Shocks with Artificial Viscosity

NASA Astrophysics Data System (ADS)

Siegler, S.; Riffert, H.

2000-03-01

We present a fully Lagrangian conservation form of the general relativistic hydrodynamic equations for perfect fluids with artificial viscosity in a given arbitrary background spacetime. This conservation formulation is achieved by choosing suitable Lagrangian time evolution variables, from which the generic fluid variables of rest-mass density, 3-velocity, and thermodynamic pressure have to be determined. We present the corresponding equations for an ideal gas and show the existence and uniqueness of the solution. On the basis of the Lagrangian formulation we have developed a three-dimensional general relativistic smoothed particle hydrodynamics (SPH) code using the standard SPH formalism as known from nonrelativistic fluid dynamics. One-dimensional simulations of a shock tube and a wall shock are presented together with a two-dimensional test calculation of an inclined shock tube. With our method we can model ultrarelativistic fluid flows including shocks with Lorentz factors of even 1000.

Dimension reduction method for SPH equations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tartakovsky, Alexandre M.; Scheibe, Timothy D.

2011-08-26

Smoothed Particle Hydrodynamics model of a complex multiscale processe often results in a system of ODEs with an enormous number of unknowns. Furthermore, a time integration of the SPH equations usually requires time steps that are smaller than the observation time by many orders of magnitude. A direct solution of these ODEs can be extremely expensive. Here we propose a novel dimension reduction method that gives an approximate solution of the SPH ODEs and provides an accurate prediction of the average behavior of the modeled system. The method consists of two main elements. First, effective equationss for evolution of averagemore » variables (e.g. average velocity, concentration and mass of a mineral precipitate) are obtained by averaging the SPH ODEs over the entire computational domain. These effective ODEs contain non-local terms in the form of volume integrals of functions of the SPH variables. Second, a computational closure is used to close the system of the effective equations. The computational closure is achieved via short bursts of the SPH model. The dimension reduction model is used to simulate flow and transport with mixing controlled reactions and mineral precipitation. An SPH model is used model transport at the porescale. Good agreement between direct solutions of the SPH equations and solutions obtained with the dimension reduction method for different boundary conditions confirms the accuracy and computational efficiency of the dimension reduction model. The method significantly accelerates SPH simulations, while providing accurate approximation of the solution and accurate prediction of the average behavior of the system.« less

Smoothed Particle Hydrodynamics: A consistent model for interfacial multiphase fluid flow simulations

NASA Astrophysics Data System (ADS)

Krimi, Abdelkader; Rezoug, Mehdi; Khelladi, Sofiane; Nogueira, Xesús; Deligant, Michael; Ramírez, Luis

2018-04-01

In this work, a consistent Smoothed Particle Hydrodynamics (SPH) model to deal with interfacial multiphase fluid flows simulation is proposed. A modification to the Continuum Stress Surface formulation (CSS) [1] to enhance the stability near the fluid interface is developed in the framework of the SPH method. A non-conservative first-order consistency operator is used to compute the divergence of stress surface tensor. This formulation benefits of all the advantages of the one proposed by Adami et al. [2] and, in addition, it can be applied to more than two phases fluid flow simulations. Moreover, the generalized wall boundary conditions [3] are modified in order to be well adapted to multiphase fluid flows with different density and viscosity. In order to allow the application of this technique to wall-bounded multiphase flows, a modification of generalized wall boundary conditions is presented here for using the SPH method. In this work we also present a particle redistribution strategy as an extension of the damping technique presented in [3] to smooth the initial transient phase of gravitational multiphase fluid flow simulations. Several computational tests are investigated to show the accuracy, convergence and applicability of the proposed SPH interfacial multiphase model.

A 3-D SPH model for simulating water flooding of a damaged floating structure

NASA Astrophysics Data System (ADS)

Guo, Kai; Sun, Peng-nan; Cao, Xue-yan; Huang, Xiao

2017-10-01

With the quasi-static analysis method, the terminal floating state of a damaged ship is usually evaluated for the risk assessment. But this is not enough since the ship has the possibility to lose its stability during the transient flooding process. Therefore, an enhanced smoothed particle hydrodynamics (SPH) model is applied in this paper to investigate the response of a simplified cabin model under the condition of the transient water flooding. The enhanced SPH model is presented firstly including the governing equations, the diffusive terms, the boundary implementations and then an algorithm regarding the coupling motions of six degrees of freedom (6-DOF) between the structure and the fluid is described. In the numerical results, a non-damaged cabin floating under the rest condition is simulated. It is shown that a stable floating state can be reached and maintained by using the present SPH scheme. After that, three-dimensional (3-D) test cases of the damaged cabin with a hole at different locations are simulated. A series of model tests are also carried out for the validation. Fairly good agreements are achieved between the numerical results and the experimental data. Relevant conclusions are drawn with respect to the mechanism of the responses of the damaged cabin model under water flooding conditions.

Three-dimensional smoothed particle hydrodynamics simulation for injection molding flow of short fiber-reinforced polymer composites

NASA Astrophysics Data System (ADS)

He, Liping; Lu, Gang; Chen, Dachuan; Li, Wenjun; Lu, Chunsheng

2017-07-01

This paper investigates the three-dimensional (3D) injection molding flow of short fiber-reinforced polymer composites using a smoothed particle hydrodynamics (SPH) simulation method. The polymer melt was modeled as a power law fluid and the fibers were considered as rigid cylindrical bodies. The filling details and fiber orientation in the injection-molding process were studied. The results indicated that the SPH method could effectively predict the order of filling, fiber accumulation, and heterogeneous distribution of fibers. The SPH simulation also showed that fibers were mainly aligned to the flow direction in the skin layer and inclined to the flow direction in the core layer. Additionally, the fiber-orientation state in the simulation was quantitatively analyzed and found to be consistent with the results calculated by conventional tensor methods.

Smoothed particle hydrodynamics with GRAPE-1A

NASA Technical Reports Server (NTRS)

Umemura, Masayuki; Fukushige, Toshiyuki; Makino, Junichiro; Ebisuzaki, Toshikazu; Sugimoto, Daiichiro; Turner, Edwin L.; Loeb, Abraham

1993-01-01

We describe the implementation of a smoothed particle hydrodynamics (SPH) scheme using GRAPE-1A, a special-purpose processor used for gravitational N-body simulations. The GRAPE-1A calculates the gravitational force exerted on a particle from all other particles in a system, while simultaneously making a list of the nearest neighbors of the particle. It is found that GRAPE-1A accelerates SPH calculations by direct summation by about two orders of magnitudes for a ten thousand-particle simulation. The effective speed is 80 Mflops, which is about 30 percent of the peak speed of GRAPE-1A. Also, in order to investigate the accuracy of GRAPE-SPH, some test simulations were executed. We found that the force and position errors are smaller than those due to representing a fluid by a finite number of particles. The total energy and momentum were conserved within 0.2-0.4 percent and 2-5 x 10 exp -5, respectively, in simulations with several thousand particles. We conclude that GRAPE-SPH is quite effective and sufficiently accurate for self-gravitating hydrodynamics.

High-resolution Hydrodynamic Simulation of Tidal Detonation of a Helium White Dwarf by an Intermediate Mass Black Hole

NASA Astrophysics Data System (ADS)

Tanikawa, Ataru

2018-05-01

We demonstrate tidal detonation during a tidal disruption event (TDE) of a helium (He) white dwarf (WD) with 0.45 M ⊙ by an intermediate mass black hole using extremely high-resolution simulations. Tanikawa et al. have shown tidal detonation in results of previous studies from unphysical heating due to low-resolution simulations, and such unphysical heating occurs in three-dimensional (3D) smoothed particle hydrodynamics (SPH) simulations even with 10 million SPH particles. In order to avoid such unphysical heating, we perform 3D SPH simulations up to 300 million SPH particles, and 1D mesh simulations using flow structure in the 3D SPH simulations for 1D initial conditions. The 1D mesh simulations have higher resolutions than the 3D SPH simulations. We show that tidal detonation occurs and confirm that this result is perfectly converged with different space resolution in both 3D SPH and 1D mesh simulations. We find that detonation waves independently arise in leading parts of the WD, and yield large amounts of 56Ni. Although detonation waves are not generated in trailing parts of the WD, the trailing parts would receive detonation waves generated in the leading parts and would leave large amounts of Si group elements. Eventually, this He WD TDE would synthesize 56Ni of 0.30 M ⊙ and Si group elements of 0.08 M ⊙, and could be observed as a luminous thermonuclear transient comparable to SNe Ia.

SPH modeling and simulation of spherical particles interacting in a viscoelastic matrix

NASA Astrophysics Data System (ADS)

Vázquez-Quesada, A.; Ellero, M.

2017-12-01

In this work, we extend the three-dimensional Smoothed Particle Hydrodynamics (SPH) non-colloidal particulate model previously developed for Newtonian suspending media in Vázquez-Quesada and Ellero ["Rheology and microstructure of non-colloidal suspensions under shear studied with smoothed particle hydrodynamics," J. Non-Newtonian Fluid Mech. 233, 37-47 (2016)] to viscoelastic matrices. For the solvent medium, the coarse-grained SPH viscoelastic formulation proposed in Vázquez-Quesada, Ellero, and Español ["Smoothed particle hydrodynamic model for viscoelastic fluids with thermal fluctuations," Phys. Rev. E 79, 056707 (2009)] is adopted. The property of this particular set of equations is that they are entirely derived within the general equation for non-equilibrium reversible-irreversible coupling formalism and therefore enjoy automatically thermodynamic consistency. The viscoelastic model is derived through a physical specification of a conformation-tensor-dependent entropy function for the fluid particles. In the simple case of suspended Hookean dumbbells, this delivers a specific SPH discretization of the Oldroyd-B constitutive equation. We validate the suspended particle model by studying the dynamics of single and mutually interacting "noncolloidal" rigid spheres under shear flow and in the presence of confinement. Numerical results agree well with available numerical and experimental data. It is straightforward to extend the particulate model to Brownian conditions and to more complex viscoelastic solvents.

SPH/N-Body simulations of small (D = 10km) asteroidal breakups and improved parametric relations for Monte-Carlo collisional models

NASA Astrophysics Data System (ADS)

Ševeček, P.; Brož, M.; Nesvorný, D.; Enke, B.; Durda, D.; Walsh, K.; Richardson, D. C.

2017-11-01

We report on our study of asteroidal breakups, i.e. fragmentations of targets, subsequent gravitational reaccumulation and formation of small asteroid families. We focused on parent bodies with diameters Dpb = 10km . Simulations were performed with a smoothed-particle hydrodynamics (SPH) code combined with an efficient N-body integrator. We assumed various projectile sizes, impact velocities and impact angles (125 runs in total). Resulting size-frequency distributions are significantly different from scaled-down simulations with Dpb = 100km targets (Durda et al., 2007). We derive new parametric relations describing fragment distributions, suitable for Monte-Carlo collisional models. We also characterize velocity fields and angular distributions of fragments, which can be used as initial conditions for N-body simulations of small asteroid families. Finally, we discuss a number of uncertainties related to SPH simulations.

A Comparison of Grid-based and SPH Binary Mass-transfer and Merger Simulations

DOE PAGES

Motl, Patrick M.; Frank, Juhan; Staff, Jan; ...

2017-03-29

There is currently a great amount of interest in the outcomes and astrophysical implications of mergers of double degenerate binaries. In a commonly adopted approximation, the components of such binaries are represented by polytropes with an index of n = 3/2. We present detailed comparisons of stellar mass-transfer and merger simulations of polytropic binaries that have been carried out using two very different numerical algorithms—a finite-volume "grid" code and a smoothed-particle hydrodynamics (SPH) code. We find that there is agreement in both the ultimate outcomes of the evolutions and the intermediate stages if the initial conditions for each code aremore » chosen to match as closely as possible. We find that even with closely matching initial setups, the time it takes to reach a concordant evolution differs between the two codes because the initial depth of contact cannot be matched exactly. There is a general tendency for SPH to yield higher mass transfer rates and faster evolution to the final outcome. Here, we also present comparisons of simulations calculated from two different energy equations: in one series, we assume a polytropic equation of state and in the other series an ideal gas equation of state. In the latter series of simulations, an atmosphere forms around the accretor, which can exchange angular momentum and cause a more rapid loss of orbital angular momentum. In the simulations presented here, the effect of the ideal equation of state is to de-stabilize the binary in both SPH and grid simulations, but the effect is more pronounced in the grid code.« less

A Comparison of Grid-based and SPH Binary Mass-transfer and Merger Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Motl, Patrick M.; Frank, Juhan; Clayton, Geoffrey C.

2017-04-01

There is currently a great amount of interest in the outcomes and astrophysical implications of mergers of double degenerate binaries. In a commonly adopted approximation, the components of such binaries are represented by polytropes with an index of n  = 3/2. We present detailed comparisons of stellar mass-transfer and merger simulations of polytropic binaries that have been carried out using two very different numerical algorithms—a finite-volume “grid” code and a smoothed-particle hydrodynamics (SPH) code. We find that there is agreement in both the ultimate outcomes of the evolutions and the intermediate stages if the initial conditions for each code are chosen to matchmore » as closely as possible. We find that even with closely matching initial setups, the time it takes to reach a concordant evolution differs between the two codes because the initial depth of contact cannot be matched exactly. There is a general tendency for SPH to yield higher mass transfer rates and faster evolution to the final outcome. We also present comparisons of simulations calculated from two different energy equations: in one series, we assume a polytropic equation of state and in the other series an ideal gas equation of state. In the latter series of simulations, an atmosphere forms around the accretor, which can exchange angular momentum and cause a more rapid loss of orbital angular momentum. In the simulations presented here, the effect of the ideal equation of state is to de-stabilize the binary in both SPH and grid simulations, but the effect is more pronounced in the grid code.« less

Implicit Incompressible SPH.

PubMed

Ihmsen, Markus; Cornelis, Jens; Solenthaler, Barbara; Horvath, Christopher; Teschner, Matthias

2013-07-25

We propose a novel formulation of the projection method for Smoothed Particle Hydrodynamics (SPH). We combine a symmetric SPH pressure force and an SPH discretization of the continuity equation to obtain a discretized form of the pressure Poisson equation (PPE). In contrast to previous projection schemes, our system does consider the actual computation of the pressure force. This incorporation improves the convergence rate of the solver. Furthermore, we propose to compute the density deviation based on velocities instead of positions as this formulation improves the robustness of the time-integration scheme. We show that our novel formulation outperforms previous projection schemes and state-of-the-art SPH methods. Large time steps and small density deviations of down to 0.01% can be handled in typical scenarios. The practical relevance of the approach is illustrated by scenarios with up to 40 million SPH particles.

Dynamic particle refinement in SPH: application to free surface flow and non-cohesive soil simulations

NASA Astrophysics Data System (ADS)

Reyes López, Yaidel; Roose, Dirk; Recarey Morfa, Carlos

2013-05-01

In this paper, we present a dynamic refinement algorithm for the smoothed particle Hydrodynamics (SPH) method. An SPH particle is refined by replacing it with smaller daughter particles, which positions are calculated by using a square pattern centered at the position of the refined particle. We determine both the optimal separation and the smoothing distance of the new particles such that the error produced by the refinement in the gradient of the kernel is small and possible numerical instabilities are reduced. We implemented the dynamic refinement procedure into two different models: one for free surface flows, and one for post-failure flow of non-cohesive soil. The results obtained for the test problems indicate that using the dynamic refinement procedure provides a good trade-off between the accuracy and the cost of the simulations.

A 1D-2D coupled SPH-SWE model applied to open channel flow simulations in complicated geometries

NASA Astrophysics Data System (ADS)

Chang, Kao-Hua; Sheu, Tony Wen-Hann; Chang, Tsang-Jung

2018-05-01

In this study, a one- and two-dimensional (1D-2D) coupled model is developed to solve the shallow water equations (SWEs). The solutions are obtained using a Lagrangian meshless method called smoothed particle hydrodynamics (SPH) to simulate shallow water flows in converging, diverging and curved channels. A buffer zone is introduced to exchange information between the 1D and 2D SPH-SWE models. Interpolated water discharge values and water surface levels at the internal boundaries are prescribed as the inflow/outflow boundary conditions in the two SPH-SWE models. In addition, instead of using the SPH summation operator, we directly solve the continuity equation by introducing a diffusive term to suppress oscillations in the predicted water depth. The performance of the two approaches in calculating the water depth is comprehensively compared through a case study of a straight channel. Additionally, three benchmark cases involving converging, diverging and curved channels are adopted to demonstrate the ability of the proposed 1D and 2D coupled SPH-SWE model through comparisons with measured data and predicted mesh-based numerical results. The proposed model provides satisfactory accuracy and guaranteed convergence.

Implicit incompressible SPH.

PubMed

Ihmsen, Markus; Cornelis, Jens; Solenthaler, Barbara; Horvath, Christopher; Teschner, Matthias

2014-03-01

We propose a novel formulation of the projection method for Smoothed Particle Hydrodynamics (SPH). We combine a symmetric SPH pressure force and an SPH discretization of the continuity equation to obtain a discretized form of the pressure Poisson equation (PPE). In contrast to previous projection schemes, our system does consider the actual computation of the pressure force. This incorporation improves the convergence rate of the solver. Furthermore, we propose to compute the density deviation based on velocities instead of positions as this formulation improves the robustness of the time-integration scheme. We show that our novel formulation outperforms previous projection schemes and state-of-the-art SPH methods. Large time steps and small density deviations of down to 0.01 percent can be handled in typical scenarios. The practical relevance of the approach is illustrated by scenarios with up to 40 million SPH particles.

Pairwise Force SPH Model for Real-Time Multi-Interaction Applications.

PubMed

Yang, Tao; Martin, Ralph R; Lin, Ming C; Chang, Jian; Hu, Shi-Min

2017-10-01

In this paper, we present a novel pairwise-force smoothed particle hydrodynamics (PF-SPH) model to enable simulation of various interactions at interfaces in real time. Realistic capture of interactions at interfaces is a challenging problem for SPH-based simulations, especially for scenarios involving multiple interactions at different interfaces. Our PF-SPH model can readily handle multiple types of interactions simultaneously in a single simulation; its basis is to use a larger support radius than that used in standard SPH. We adopt a novel anisotropic filtering term to further improve the performance of interaction forces. The proposed model is stable; furthermore, it avoids the particle clustering problem which commonly occurs at the free surface. We show how our model can be used to capture various interactions. We also consider the close connection between droplets and bubbles, and show how to animate bubbles rising in liquid as well as bubbles in air. Our method is versatile, physically plausible and easy-to-implement. Examples are provided to demonstrate the capabilities and effectiveness of our approach.

Motion of dust particles in nonuniform magnetic field and applicability of smoothed particle hydrodynamics simulation

NASA Astrophysics Data System (ADS)

Saitou, Y.

2018-01-01

An SPH (Smoothed Particle Hydrodynamics) simulation code is developed to reproduce our findings on behavior of dust particles, which were obtained in our previous experiments (Phys. Plasmas, 23, 013709 (2016) and Abst. 18th Intern. Cong. Plasma Phys. (Kaohsiung, 2016)). Usually, in an SPH simulation, a smoothed particle is interpreted as a discretized fluid element. Here we regard the particles as dust particles because it is known that behavior of dust particles in complex plasmas can be described using fluid dynamics equations in many cases. Various rotation velocities that are difficult to achieve in the experiment are given to particles at boundaries in the newly developed simulation and motion of particles is investigated. Preliminary results obtained by the simulation are shown.

Two-dimensional free-surface flow under gravity: A new benchmark case for SPH method

NASA Astrophysics Data System (ADS)

Wu, J. Z.; Fang, L.

2018-02-01

Currently there are few free-surface benchmark cases with analytical results for the Smoothed Particle Hydrodynamics (SPH) simulation. In the present contribution we introduce a two-dimensional free-surface flow under gravity, and obtain an analytical expression on the surface height difference and a theoretical estimation on the surface fractal dimension. They are preliminarily validated and supported by SPH calculations.

SPH modeling of fluid-structure interaction

NASA Astrophysics Data System (ADS)

Han, Luhui; Hu, Xiangyu

2018-02-01

This work concerns numerical modeling of fluid-structure interaction (FSI) problems in a uniform smoothed particle hydrodynamics (SPH) framework. It combines a transport-velocity SPH scheme, advancing fluid motions, with a total Lagrangian SPH formulation dealing with the structure deformations. Since both fluid and solid governing equations are solved in SPH framework, while coupling becomes straightforward, the momentum conservation of the FSI system is satisfied strictly. A well-known FSI benchmark test case has been performed to validate the modeling and to demonstrate its potential.

Nuclear subsurface explosion modeling and hydrodynamic fragmentation simulation of hazardous asteroids

NASA Astrophysics Data System (ADS)

Premaratne, Pavithra Dhanuka

Disruption and fragmentation of an asteroid using nuclear explosive devices (NEDs) is a highly complex yet a practical solution to mitigating the impact threat of asteroids with short warning time. A Hypervelocity Asteroid Intercept Vehicle (HAIV) concept, developed at the Asteroid Deflection Research Center (ADRC), consists of a primary vehicle that acts as kinetic impactor and a secondary vehicle that houses NEDs. The kinetic impactor (lead vehicle) strikes the asteroid creating a crater. The secondary vehicle will immediately enter the crater and detonate its nuclear payload creating a blast wave powerful enough to fragment the asteroid. The nuclear subsurface explosion modeling and hydrodynamic simulation has been a challenging research goal that paves the way an array of mission critical information. A mesh-free hydrodynamic simulation method, Smoothed Particle Hydrodynamics (SPH) was utilized to obtain both qualitative and quantitative solutions for explosion efficiency. Commercial fluid dynamics packages such as AUTODYN along with the in-house GPU accelerated SPH algorithms were used to validate and optimize high-energy explosion dynamics for a variety of test cases. Energy coupling from the NED to the target body was also examined to determine the effectiveness of nuclear subsurface explosions. Success of a disruption mission also depends on the survivability of the nuclear payload when the secondary vehicle approaches the newly formed crater at a velocity of 10 km/s or higher. The vehicle may come into contact with debris ejecting the crater which required the conceptual development of a Whipple shield. As the vehicle closes on the crater, its skin may also experience extreme temperatures due to heat radiated from the crater bottom. In order to address this thermal problem, a simple metallic thermal shield design was implemented utilizing a radiative heat transfer algorithm and nodal solutions obtained from hydrodynamic simulations.

Smooth Particle Hydrodynamics GPU-Acceleration Tool for Asteroid Fragmentation Simulation

NASA Astrophysics Data System (ADS)

Buruchenko, Sergey K.; Schäfer, Christoph M.; Maindl, Thomas I.

2017-10-01

The impact threat of near-Earth objects (NEOs) is a concern to the global community, as evidenced by the Chelyabinsk event (caused by a 17-m meteorite) in Russia on February 15, 2013 and a near miss by asteroid 2012 DA14 ( 30 m diameter), on the same day. The expected energy, from either a low-altitude air burst or direct impact, would have severe consequences, especially in populated regions. To mitigate this threat one of the methods is employment of large kinetic-energy impactors (KEIs). The simulation of asteroid target fragmentation is a challenging task which demands efficient and accurate numerical methods with large computational power. Modern graphics processing units (GPUs) lead to a major increase 10 times and more in the performance of the computation of astrophysical and high velocity impacts. The paper presents a new implementation of the numerical method smooth particle hydrodynamics (SPH) using NVIDIA-GPU and the first astrophysical and high velocity application of the new code. The code allows for a tremendous increase in speed of astrophysical simulations with SPH and self-gravity at low costs for new hardware. We have implemented the SPH equations to model gas, liquids and elastic, and plastic solid bodies and added a fragmentation model for brittle materials. Self-gravity may be optionally included in the simulations.

Comparison of ALE and SPH Methods for Simulating Mine Blast Effects on Structures

DTIC Science & Technology

2010-12-01

Comparison of ALE and SPH methods for simulating mine blast effects on struc- tures Geneviève Toussaint Amal Bouamoul DRDC Valcartier Defence R&D...Canada – Valcartier Technical Report DRDC Valcartier TR 2010-326 December 2010 Comparison of ALE and SPH methods for simulating mine blast...Valcartier TR 2010-326 iii Executive summary Comparison of ALE and SPH methods for simulating mine blast effects on structures

X-ray Modeling of η Carinae & WR140 from SPH Simulations

NASA Astrophysics Data System (ADS)

Russell, Christopher M. P.; Corcoran, Michael F.; Okazaki, Atsuo T.; Madura, Thomas I.; Owocki, Stanley P.

2011-01-01

The colliding wind binary (CWB) systems η Carinae and WR140 provide unique laboratories for X-ray astrophysics. Their wind-wind collisions produce hard X-rays that have been monitored extensively by several X-ray telescopes, including RXTE. To interpret these RXTE X-ray light curves, we model the wind-wind collision using 3D smoothed particle hydrodynamics (SPH) simulations. Adiabatic simulations that account for the emission and absorption of X-rays from an assumed point source at the apex of the wind-collision shock cone by the distorted winds can closely match the observed 2-10keV RXTE light curves of both η Car and WR140. This point-source model can also explain the early recovery of η Car's X-ray light curve from the 2009.0 minimum by a factor of 2-4 reduction in the mass loss rate of η Car. Our more recent models relax the point-source approximation and account for the spatially extended emission along the wind-wind interaction shock front. For WR140, the computed X-ray light curve again matches the RXTE observations quite well. But for η Car, a hot, post-periastron bubble leads to an emission level that does not match the extended X-ray minimum observed by RXTE. Initial results from incorporating radiative cooling and radiatively-driven wind acceleration via a new anti-gravity approach into the SPH code are also discussed.

SPH Modelling of Sea-ice Pack Dynamics

NASA Astrophysics Data System (ADS)

Staroszczyk, Ryszard

2017-12-01

The paper is concerned with the problem of sea-ice pack motion and deformation under the action of wind and water currents. Differential equations describing the dynamics of ice, with its very distinct mateFfigrial responses in converging and diverging flows, express the mass and linear momentum balances on the horizontal plane (the free surface of the ocean). These equations are solved by the fully Lagrangian method of smoothed particle hydrodynamics (SPH). Assuming that the ice behaviour can be approximated by a non-linearly viscous rheology, the proposed SPH model has been used to simulate the evolution of a sea-ice pack driven by wind drag stresses. The results of numerical simulations illustrate the evolution of an ice pack, including variations in ice thickness and ice area fraction in space and time. The effects of different initial ice pack configurations and of different conditions assumed at the coast-ice interface are examined. In particular, the SPH model is applied to a pack flow driven by a vortex wind to demonstrate how well the Lagrangian formulation can capture large deformations and displacements of sea ice.

3D SPH numerical simulation of the wave generated by the Vajont rockslide

NASA Astrophysics Data System (ADS)

Vacondio, R.; Mignosa, P.; Pagani, S.

2013-09-01

A 3D numerical modeling of the wave generated by the Vajont slide, one of the most destructive ever occurred, is presented in this paper. A meshless Lagrangian Smoothed Particle Hydrodynamics (SPH) technique was adopted to simulate the highly fragmented violent flow generated by the falling slide in the artificial reservoir. The speed-up achievable via General Purpose Graphic Processing Units (GP-GPU) allowed to adopt the adequate resolution to describe the phenomenon. The comparison with the data available in literature showed that the results of the numerical simulation reproduce satisfactorily the maximum run-up, also the water surface elevation in the residual lake after the event. Moreover, the 3D velocity field of the flow during the event and the discharge hydrograph which overtopped the dam, were obtained.

Simulation of impact ballistic of Cu-10wt%Sn frangible bullet using smoothed particle hydrodynamics

NASA Astrophysics Data System (ADS)

Hidayat, Mas Irfan P.; Widyastuti, Simaremare, Peniel

2018-04-01

Frangible bullet is designed to disintegrate upon impact against a hard target. Understanding the impact response and performance of frangible bullet is therefore of highly interest. In this paper, simulation of impact ballistic of Cu-IOwt%Sn frangible bullet using smoothed particle hydrodynamics (SPH) method is presented. The frangible bullet is impacted against a hard, cylindrical stainless steel target. Effect of variability of the frangible bullet material properties due to the variation of sintering temperature in its manufacturing process to the bullet frangibility factor (FF) is investigated numerically. In addition, the bullet kinetic energy during impact as well as its ricochet and fragmentation are also examined and simulated. Failure criterion based upon maximum strain is employed in the simulation. It is shown that the SPH simulation can produce good estimation for kinetic energy of bullet after impact, thus giving the FF prediction with respect to the variation of frangible bullet material properties. In comparison to explicit finite element (FE) simulation, in which only material/element deletion is shown, convenience in showing frangible bullet fragmentation is shown using the SPH simulation. As a result, the effect of sintering temperature to the way of the frangible bullet fragmented can be also observed clearly.

Hydrodynamic simulations with the Godunov smoothed particle hydrodynamics

NASA Astrophysics Data System (ADS)

Murante, G.; Borgani, S.; Brunino, R.; Cha, S.-H.

2011-10-01

We present results based on an implementation of the Godunov smoothed particle hydrodynamics (GSPH), originally developed by Inutsuka, in the GADGET-3 hydrodynamic code. We first review the derivation of the GSPH discretization of the equations of moment and energy conservation, starting from the convolution of these equations with the interpolating kernel. The two most important aspects of the numerical implementation of these equations are (a) the appearance of fluid velocity and pressure obtained from the solution of the Riemann problem between each pair of particles, and (b) the absence of an artificial viscosity term. We carry out three different controlled hydrodynamical three-dimensional tests, namely the Sod shock tube, the development of Kelvin-Helmholtz instabilities in a shear-flow test and the 'blob' test describing the evolution of a cold cloud moving against a hot wind. The results of our tests confirm and extend in a number of aspects those recently obtained by Cha, Inutsuka & Nayakshin: (i) GSPH provides a much improved description of contact discontinuities, with respect to smoothed particle hydrodynamics (SPH), thus avoiding the appearance of spurious pressure forces; (ii) GSPH is able to follow the development of gas-dynamical instabilities, such as the Kevin-Helmholtz and the Rayleigh-Taylor ones; (iii) as a result, GSPH describes the development of curl structures in the shear-flow test and the dissolution of the cold cloud in the 'blob' test. Besides comparing the results of GSPH with those from standard SPH implementations, we also discuss in detail the effect on the performances of GSPH of changing different aspects of its implementation: choice of the number of neighbours, accuracy of the interpolation procedure to locate the interface between two fluid elements (particles) for the solution of the Riemann problem, order of the reconstruction for the assignment of variables at the interface, choice of the limiter to prevent oscillations of

Computational performance of a smoothed particle hydrodynamics simulation for shared-memory parallel computing

NASA Astrophysics Data System (ADS)

Nishiura, Daisuke; Furuichi, Mikito; Sakaguchi, Hide

2015-09-01

The computational performance of a smoothed particle hydrodynamics (SPH) simulation is investigated for three types of current shared-memory parallel computer devices: many integrated core (MIC) processors, graphics processing units (GPUs), and multi-core CPUs. We are especially interested in efficient shared-memory allocation methods for each chipset, because the efficient data access patterns differ between compute unified device architecture (CUDA) programming for GPUs and OpenMP programming for MIC processors and multi-core CPUs. We first introduce several parallel implementation techniques for the SPH code, and then examine these on our target computer architectures to determine the most effective algorithms for each processor unit. In addition, we evaluate the effective computing performance and power efficiency of the SPH simulation on each architecture, as these are critical metrics for overall performance in a multi-device environment. In our benchmark test, the GPU is found to produce the best arithmetic performance as a standalone device unit, and gives the most efficient power consumption. The multi-core CPU obtains the most effective computing performance. The computational speed of the MIC processor on Xeon Phi approached that of two Xeon CPUs. This indicates that using MICs is an attractive choice for existing SPH codes on multi-core CPUs parallelized by OpenMP, as it gains computational acceleration without the need for significant changes to the source code.

SPH Simulation of Impact of a Surge on a Wall

NASA Astrophysics Data System (ADS)

Diwakar, Manoj Kumar; Mohapatra, Pranab Kumar; Tripathi, Shivam

2014-05-01

Structures located on the downstream of a dam are prone to impact of the surge due to dam break flow. Ramsden (1996) experimentally studied the run-up height on a vertical wall due to propagation of bore and surge on dry bed and measured their impact on the wall. Mohapatra et al. (2000) applied Navier Stokes equations to numerically study the impact of bore on vertical and inclined walls. They also obtained the evolution of surge on dry bed. In the present work, the impact of a surge wave due to dam break flow against the wall is modeled with a two-dimensional smoothed particle hydrodynamics (SPH) model. SPH is a mesh-free method that relies on the particle view of the field problem and approximates the continuity and momentum equations on a set of particles. The method solves the strong form of Navier-Stokes equations. The governing equations are solved numerically in the vertical plane. The propagation of the surge wave, its impact and the maximum run-up on the wall located at the boundary are analyzed. Surface profile, velocity field and pressure distributions are simulated. Non-dimensional run-up height obtained from the present numerical model is 0.86 and is in good agreement with the available experimental data of Ramsden (1996) which is in the range of 0.75-0.9. Also, the simulated profile of the surge tip was comparable to the empirical equations refereed in Ramsden (1996). The model is applied to the study the maximum force and the run-up height on inclined walls with different inclinations. The results indicate that the maximum force and the run-up height on the wall increase with the increment of wall inclination. Comparison of numerical results with analytical solutions derived from shallow water equations clearly shows the breakdown of shallow water assumption during the impact. In addition to these results, the numerical simulation yields the complete velocity and pressure ?elds which may be used to design structures located in the path of a dam

SPH non-Newtonian Model for Ice Sheet and Ice Shelf Dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tartakovsky, Alexandre M.; Pan, Wenxiao; Monaghan, Joseph J.

2012-07-07

We propose a new three-dimensional smoothed particle hydrodynamics (SPH) non-Newtonian model to study coupled ice sheet and ice shelf dynamics. Most existing ice sheet numerical models use a grid-based Eulerian approach, and are usually restricted to shallow ice sheet and ice shelf approximations of the momentum conservation equation. SPH, a fully Lagrangian particle method, solves the full momentum conservation equation. SPH method also allows modeling of free-surface flows, large material deformation, and material fragmentation without employing complex front-tracking schemes, and does not require re-meshing. As a result, SPH codes are highly scalable. Numerical accuracy of the proposed SPH model ismore » first verified by simulating a plane shear flow with a free surface and the propagation of a blob of ice along a horizontal surface. Next, the SPH model is used to investigate the grounding line dynamics of ice sheet/shelf. The steady position of the grounding line, obtained from our SPH simulations, is in good agreement with laboratory observations for a wide range of bedrock slopes, ice-to-fluid density ratios, and flux. We examine the effect of non-Newtonian behavior of ice on the grounding line dynamics. The non-Newtonian constitutive model is based on Glen's law for a creeping flow of a polycrystalline ice. Finally, we investigate the effect of a bedrock geometry on a steady-state position of the grounding line.« less

Characterizing flow in oil reservoir rock using SPH: absolute permeability

NASA Astrophysics Data System (ADS)

Holmes, David W.; Williams, John R.; Tilke, Peter; Leonardi, Christopher R.

2016-04-01

In this paper, a three-dimensional smooth particle hydrodynamics (SPH) simulator for modeling grain scale fluid flow in porous rock is presented. The versatility of the SPH method has driven its use in increasingly complex areas of flow analysis, including flows related to permeable rock for both groundwater and petroleum reservoir research. While previous approaches to such problems using SPH have involved the use of idealized pore geometries (cylinder/sphere packs etc), in this paper we detail the characterization of flow in models with geometries taken from 3D X-ray microtomographic imaging of actual porous rock; specifically 25.12 % porosity dolomite. This particular rock type has been well characterized experimentally and described in the literature, thus providing a practical `real world' means of verification of SPH that will be key to its acceptance by industry as a viable alternative to traditional reservoir modeling tools. The true advantages of SPH are realized when adding the complexity of multiple fluid phases, however, the accuracy of SPH for single phase flow is, as yet, under developed in the literature and will be the primary focus of this paper. Flow in reservoir rock will typically occur in the range of low Reynolds numbers, making the enforcement of no-slip boundary conditions an important factor in simulation. To this end, we detail the development of a new, robust, and numerically efficient method for implementing no-slip boundary conditions in SPH that can handle the degree of complexity of boundary surfaces, characteristic of an actual permeable rock sample. A study of the effect of particle density is carried out and simulation results for absolute permeability are presented and compared to those from experimentation showing good agreement and validating the method for such applications.

A technique to remove the tensile instability in weakly compressible SPH

NASA Astrophysics Data System (ADS)

Xu, Xiaoyang; Yu, Peng

2018-01-01

When smoothed particle hydrodynamics (SPH) is directly applied for the numerical simulations of transient viscoelastic free surface flows, a numerical problem called tensile instability arises. In this paper, we develop an optimized particle shifting technique to remove the tensile instability in SPH. The basic equations governing free surface flow of an Oldroyd-B fluid are considered, and approximated by an improved SPH scheme. This includes the implementations of the correction of kernel gradient and the introduction of Rusanov flux into the continuity equation. To verify the effectiveness of the optimized particle shifting technique in removing the tensile instability, the impacting drop, the injection molding of a C-shaped cavity, and the extrudate swell, are conducted. The numerical results obtained are compared with those simulated by other numerical methods. A comparison among different numerical techniques (e.g., the artificial stress) to remove the tensile instability is further performed. All numerical results agree well with the available data.

Continuum modeling of rate-dependent granular flows in SPH

DOE PAGES

Hurley, Ryan C.; Andrade, José E.

2016-09-13

In this paper, we discuss a constitutive law for modeling rate-dependent granular flows that has been implemented in smoothed particle hydrodynamics (SPH). We model granular materials using a viscoplastic constitutive law that produces a Drucker–Prager-like yield condition in the limit of vanishing flow. A friction law for non-steady flows, incorporating rate-dependence and dilation, is derived and implemented within the constitutive law. We compare our SPH simulations with experimental data, demonstrating that they can capture both steady and non-steady dynamic flow behavior, notably including transient column collapse profiles. In conclusion, this technique may therefore be attractive for modeling the time-dependent evolutionmore » of natural and industrial flows.« less

ZENO: N-body and SPH Simulation Codes

NASA Astrophysics Data System (ADS)

Barnes, Joshua E.

2011-02-01

The ZENO software package integrates N-body and SPH simulation codes with a large array of programs to generate initial conditions and analyze numerical simulations. Written in C, the ZENO system is portable between Mac, Linux, and Unix platforms. It is in active use at the Institute for Astronomy (IfA), at NRAO, and possibly elsewhere. Zeno programs can perform a wide range of simulation and analysis tasks. While many of these programs were first created for specific projects, they embody algorithms of general applicability and embrace a modular design strategy, so existing code is easily applied to new tasks. Major elements of the system include: Structured data file utilities facilitate basic operations on binary data, including import/export of ZENO data to other systems.Snapshot generation routines create particle distributions with various properties. Systems with user-specified density profiles can be realized in collisionless or gaseous form; multiple spherical and disk components may be set up in mutual equilibrium.Snapshot manipulation routines permit the user to sift, sort, and combine particle arrays, translate and rotate particle configurations, and assign new values to data fields associated with each particle.Simulation codes include both pure N-body and combined N-body/SPH programs: Pure N-body codes are available in both uniprocessor and parallel versions.SPH codes offer a wide range of options for gas physics, including isothermal, adiabatic, and radiating models. Snapshot analysis programs calculate temporal averages, evaluate particle statistics, measure shapes and density profiles, compute kinematic properties, and identify and track objects in particle distributions.Visualization programs generate interactive displays and produce still images and videos of particle distributions; the user may specify arbitrary color schemes and viewing transformations.

IMPROVED PERFORMANCES IN SUBSONIC FLOWS OF AN SPH SCHEME WITH GRADIENTS ESTIMATED USING AN INTEGRAL APPROACH

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valdarnini, R., E-mail: valda@sissa.it

In this paper, we present results from a series of hydrodynamical tests aimed at validating the performance of a smoothed particle hydrodynamics (SPH) formulation in which gradients are derived from an integral approach. We specifically investigate the code behavior with subsonic flows, where it is well known that zeroth-order inconsistencies present in standard SPH make it particularly problematic to correctly model the fluid dynamics. In particular, we consider the Gresho–Chan vortex problem, the growth of Kelvin–Helmholtz instabilities, the statistics of driven subsonic turbulence and the cold Keplerian disk problem. We compare simulation results for the different tests with those obtained,more » for the same initial conditions, using standard SPH. We also compare the results with the corresponding ones obtained previously with other numerical methods, such as codes based on a moving-mesh scheme or Godunov-type Lagrangian meshless methods. We quantify code performances by introducing error norms and spectral properties of the particle distribution, in a way similar to what was done in other works. We find that the new SPH formulation exhibits strongly reduced gradient errors and outperforms standard SPH in all of the tests considered. In fact, in terms of accuracy, we find good agreement between the simulation results of the new scheme and those produced using other recently proposed numerical schemes. These findings suggest that the proposed method can be successfully applied for many astrophysical problems in which the presence of subsonic flows previously limited the use of SPH, with the new scheme now being competitive in these regimes with other numerical methods.« less

Equalizing resolution in smoothed-particle hydrodynamics calculations using self-adaptive sinc kernels

NASA Astrophysics Data System (ADS)

García-Senz, Domingo; Cabezón, Rubén M.; Escartín, José A.; Ebinger, Kevin

2014-10-01

Context. The smoothed-particle hydrodynamics (SPH) technique is a numerical method for solving gas-dynamical problems. It has been applied to simulate the evolution of a wide variety of astrophysical systems. The method has a second-order accuracy, with a resolution that is usually much higher in the compressed regions than in the diluted zones of the fluid. Aims: We propose and check a method to balance and equalize the resolution of SPH between high- and low-density regions. This method relies on the versatility of a family of interpolators called sinc kernels, which allows increasing the interpolation quality by varying only a single parameter (the exponent of the sinc function). Methods: The proposed method was checked and validated through a number of numerical tests, from standard one-dimensional Riemann problems in shock tubes, to multidimensional simulations of explosions, hydrodynamic instabilities, and the collapse of a Sun-like polytrope. Results: The analysis of the hydrodynamical simulations suggests that the scheme devised to equalize the accuracy improves the treatment of the post-shock regions and, in general, of the rarefacted zones of fluids while causing no harm to the growth of hydrodynamic instabilities. The method is robust and easy to implement with a low computational overload. It conserves mass, energy, and momentum and reduces to the standard SPH scheme in regions of the fluid that have smooth density gradients.

Thermomechanically coupled conduction mode laser welding simulations using smoothed particle hydrodynamics

NASA Astrophysics Data System (ADS)

Hu, Haoyue; Eberhard, Peter

2017-10-01

Process simulations of conduction mode laser welding are performed using the meshless Lagrangian smoothed particle hydrodynamics (SPH) method. The solid phase is modeled based on the governing equations in thermoelasticity. For the liquid phase, surface tension effects are taken into account to simulate the melt flow in the weld pool, including the Marangoni force caused by a temperature-dependent surface tension gradient. A non-isothermal solid-liquid phase transition with the release or absorption of additional energy known as the latent heat of fusion is considered. The major heat transfer through conduction is modeled, whereas heat convection and radiation are neglected. The energy input from the laser beam is modeled as a Gaussian heat source acting on the initial material surface. The developed model is implemented in Pasimodo. Numerical results obtained with the model are presented for laser spot welding and seam welding of aluminum and iron. The change of process parameters like welding speed and laser power, and their effects on weld dimensions are investigated. Furthermore, simulations may be useful to obtain the threshold for deep penetration welding and to assess the overall welding quality. A scalability and performance analysis of the implemented SPH algorithm in Pasimodo is run in a shared memory environment. The analysis reveals the potential of large welding simulations on multi-core machines.

Smoothed particle hydrodynamics method for evaporating multiphase flows.

PubMed

Yang, Xiufeng; Kong, Song-Charng

2017-09-01

The smoothed particle hydrodynamics (SPH) method has been increasingly used for simulating fluid flows; however, its ability to simulate evaporating flow requires significant improvements. This paper proposes an SPH method for evaporating multiphase flows. The present SPH method can simulate the heat and mass transfers across the liquid-gas interfaces. The conservation equations of mass, momentum, and energy were reformulated based on SPH, then were used to govern the fluid flow and heat transfer in both the liquid and gas phases. The continuity equation of the vapor species was employed to simulate the vapor mass fraction in the gas phase. The vapor mass fraction at the interface was predicted by the Clausius-Clapeyron correlation. An evaporation rate was derived to predict the mass transfer from the liquid phase to the gas phase at the interface. Because of the mass transfer across the liquid-gas interface, the mass of an SPH particle was allowed to change. Alternative particle splitting and merging techniques were developed to avoid large mass difference between SPH particles of the same phase. The proposed method was tested by simulating three problems, including the Stefan problem, evaporation of a static drop, and evaporation of a drop impacting a hot surface. For the Stefan problem, the SPH results of the evaporation rate at the interface agreed well with the analytical solution. For drop evaporation, the SPH result was compared with the result predicted by a level-set method from the literature. In the case of drop impact on a hot surface, the evolution of the shape of the drop, temperature, and vapor mass fraction were predicted.

SPH with dynamical smoothing length adjustment based on the local flow kinematics

NASA Astrophysics Data System (ADS)

Olejnik, Michał; Szewc, Kamil; Pozorski, Jacek

2017-11-01

Due to the Lagrangian nature of Smoothed Particle Hydrodynamics (SPH), the adaptive resolution remains a challenging task. In this work, we first analyse the influence of the simulation parameters and the smoothing length on solution accuracy, in particular in high strain regions. Based on this analysis we develop a novel approach to dynamically adjust the kernel range for each SPH particle separately, accounting for the local flow kinematics. We use the Okubo-Weiss parameter that distinguishes the strain and vorticity dominated regions in the flow domain. The proposed development is relatively simple and implies only a moderate computational overhead. We validate the modified SPH algorithm for a selection of two-dimensional test cases: the Taylor-Green flow, the vortex spin-down, the lid-driven cavity and the dam-break flow against a sharp-edged obstacle. The simulation results show good agreement with the reference data and improvement of the long-term accuracy for unsteady flows. For the lid-driven cavity case, the proposed dynamical adjustment remedies the problem of tensile instability (particle clustering).

Pairwise Force Smoothed Particle Hydrodynamics model for multiphase flow: Surface tension and contact line dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tartakovsky, Alexandre M.; Panchenko, Alexander

2016-01-01

We present a novel formulation of the Pairwise Force Smoothed Particle Hydrodynamics Model (PF-SPH) and use it to simulate two- and three-phase flows in bounded domains. In the PF-SPH model, the Navier-Stokes equations are discretized with the Smoothed Particle Hydrodynamics (SPH) method and the Young-Laplace boundary condition at the fluid-fluid interface and the Young boundary condition at the fluid-fluid-solid interface are replaced with pairwise forces added into the Navier-Stokes equations. We derive a relationship between the parameters in the pairwise forces and the surface tension and static contact angle. Next, we demonstrate the accuracy of the model under static andmore » dynamic conditions. Finally, to demonstrate the capabilities and robustness of the model we use it to simulate flow of three fluids in a porous material.« less

Dynamic simulations of geologic materials using combined FEM/DEM/SPH analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morris, J P; Johnson, S M

2008-03-26

An overview of the Lawrence Discrete Element Code (LDEC) is presented, and results from a study investigating the effect of explosive and impact loading on geologic materials using the Livermore Distinct Element Code (LDEC) are detailed. LDEC was initially developed to simulate tunnels and other structures in jointed rock masses using large numbers of polyhedral blocks. Many geophysical applications, such as projectile penetration into rock, concrete targets, and boulder fields, require a combination of continuum and discrete methods in order to predict the formation and interaction of the fragments produced. In an effort to model this class of problems, LDECmore » now includes implementations of Cosserat point theory and cohesive elements. This approach directly simulates the transition from continuum to discontinuum behavior, thereby allowing for dynamic fracture within a combined finite element/discrete element framework. In addition, there are many application involving geologic materials where fluid-structure interaction is important. To facilitate solution of this class of problems a Smooth Particle Hydrodynamics (SPH) capability has been incorporated into LDEC to simulate fully coupled systems involving geologic materials and a saturating fluid. We will present results from a study of a broad range of geomechanical problems that exercise the various components of LDEC in isolation and in tandem.« less

SPH/N-body simulations of small (D = 10 km) monolithic asteroidal breakups and improved parametric relations for Monte-Carlo collisional models

NASA Astrophysics Data System (ADS)

Ševecek, Pavel; Broz, Miroslav; Nesvorny, David; Durda, Daniel D.; Asphaug, Erik; Walsh, Kevin J.; Richardson, Derek C.

2016-10-01

Detailed models of asteroid collisions can yield important constrains for the evolution of the Main Asteroid Belt, but the respective parameter space is large and often unexplored. We thus performed a new set of simulations of asteroidal breakups, i.e. fragmentations of intact targets, subsequent gravitational reaccumulation and formation of small asteroid families, focusing on parent bodies with diameters D = 10 km.Simulations were performed with a smoothed-particle hydrodynamics (SPH) code (Benz & Asphaug 1994), combined with an efficient N-body integrator (Richardson et al. 2000). We assumed a number of projectile sizes, impact velocities and impact angles. The rheology used in the physical model does not include friction nor crushing; this allows for a direct comparison to results of Durda et al. (2007). Resulting size-frequency distributions are significantly different from scaled-down simulations with D = 100 km monolithic targets, although they may be even more different for pre-shattered targets.We derive new parametric relations describing fragment distributions, suitable for Monte-Carlo collisional models. We also characterize velocity fields and angular distributions of fragments, which can be used as initial conditions in N-body simulations of small asteroid families. Finally, we discuss various uncertainties related to SPH simulations.

Deformation of Soft Tissue and Force Feedback Using the Smoothed Particle Hydrodynamics

PubMed Central

Liu, Xuemei; Wang, Ruiyi; Li, Yunhua; Song, Dongdong

2015-01-01

We study the deformation and haptic feedback of soft tissue in virtual surgery based on a liver model by using a force feedback device named PHANTOM OMNI developed by SensAble Company in USA. Although a significant amount of research efforts have been dedicated to simulating the behaviors of soft tissue and implementing force feedback, it is still a challenging problem. This paper introduces a kind of meshfree method for deformation simulation of soft tissue and force computation based on viscoelastic mechanical model and smoothed particle hydrodynamics (SPH). Firstly, viscoelastic model can present the mechanical characteristics of soft tissue which greatly promotes the realism. Secondly, SPH has features of meshless technique and self-adaption, which supply higher precision than methods based on meshes for force feedback computation. Finally, a SPH method based on dynamic interaction area is proposed to improve the real time performance of simulation. The results reveal that SPH methodology is suitable for simulating soft tissue deformation and force feedback calculation, and SPH based on dynamic local interaction area has a higher computational efficiency significantly compared with usual SPH. Our algorithm has a bright prospect in the area of virtual surgery. PMID:26417380

Divergence-Free SPH for Incompressible and Viscous Fluids.

PubMed

Bender, Jan; Koschier, Dan

2017-03-01

In this paper we present a novel Smoothed Particle Hydrodynamics (SPH) method for the efficient and stable simulation of incompressible fluids. The most efficient SPH-based approaches enforce incompressibility either on position or velocity level. However, the continuity equation for incompressible flow demands to maintain a constant density and a divergence-free velocity field. We propose a combination of two novel implicit pressure solvers enforcing both a low volume compression as well as a divergence-free velocity field. While a compression-free fluid is essential for realistic physical behavior, a divergence-free velocity field drastically reduces the number of required solver iterations and increases the stability of the simulation significantly. Thanks to the improved stability, our method can handle larger time steps than previous approaches. This results in a substantial performance gain since the computationally expensive neighborhood search has to be performed less frequently. Moreover, we introduce a third optional implicit solver to simulate highly viscous fluids which seamlessly integrates into our solver framework. Our implicit viscosity solver produces realistic results while introducing almost no numerical damping. We demonstrate the efficiency, robustness and scalability of our method in a variety of complex simulations including scenarios with millions of turbulent particles or highly viscous materials.

gpuSPHASE-A shared memory caching implementation for 2D SPH using CUDA

NASA Astrophysics Data System (ADS)

Winkler, Daniel; Meister, Michael; Rezavand, Massoud; Rauch, Wolfgang

2017-04-01

Smoothed particle hydrodynamics (SPH) is a meshless Lagrangian method that has been successfully applied to computational fluid dynamics (CFD), solid mechanics and many other multi-physics problems. Using the method to solve transport phenomena in process engineering requires the simulation of several days to weeks of physical time. Based on the high computational demand of CFD such simulations in 3D need a computation time of years so that a reduction to a 2D domain is inevitable. In this paper gpuSPHASE, a new open-source 2D SPH solver implementation for graphics devices, is developed. It is optimized for simulations that must be executed with thousands of frames per second to be computed in reasonable time. A novel caching algorithm for Compute Unified Device Architecture (CUDA) shared memory is proposed and implemented. The software is validated and the performance is evaluated for the well established dambreak test case.

A new class of accurate, mesh-free hydrodynamic simulation methods

NASA Astrophysics Data System (ADS)

Hopkins, Philip F.

2015-06-01

We present two new Lagrangian methods for hydrodynamics, in a systematic comparison with moving-mesh, smoothed particle hydrodynamics (SPH), and stationary (non-moving) grid methods. The new methods are designed to simultaneously capture advantages of both SPH and grid-based/adaptive mesh refinement (AMR) schemes. They are based on a kernel discretization of the volume coupled to a high-order matrix gradient estimator and a Riemann solver acting over the volume `overlap'. We implement and test a parallel, second-order version of the method with self-gravity and cosmological integration, in the code GIZMO:1 this maintains exact mass, energy and momentum conservation; exhibits superior angular momentum conservation compared to all other methods we study; does not require `artificial diffusion' terms; and allows the fluid elements to move with the flow, so resolution is automatically adaptive. We consider a large suite of test problems, and find that on all problems the new methods appear competitive with moving-mesh schemes, with some advantages (particularly in angular momentum conservation), at the cost of enhanced noise. The new methods have many advantages versus SPH: proper convergence, good capturing of fluid-mixing instabilities, dramatically reduced `particle noise' and numerical viscosity, more accurate sub-sonic flow evolution, and sharp shock-capturing. Advantages versus non-moving meshes include: automatic adaptivity, dramatically reduced advection errors and numerical overmixing, velocity-independent errors, accurate coupling to gravity, good angular momentum conservation and elimination of `grid alignment' effects. We can, for example, follow hundreds of orbits of gaseous discs, while AMR and SPH methods break down in a few orbits. However, fixed meshes minimize `grid noise'. These differences are important for a range of astrophysical problems.

Multicale modeling of the detonation of aluminized explosives using SPH-MD-QM method

NASA Astrophysics Data System (ADS)

Peng, Qing; Wang, Guangyu; Liu, Gui-Rong; de, Suvranu

Aluminized explosives have been applied in military industry since decades ago. Compared with ideal explosives, aluminized explosives feature both fast detonation and slow metal combustion chemistry, generating a complex multi-phase reactive flow. Here, we introduce a sequential multiscale model of SPH-MD-QM to simulate the detonation behavior of aluminized explosives. At the bottom level, first-principles quantum mechanics (QM) calculations are employed to obtain the training sets for fitting the ReaxFF potentials, which are used in turn in the reactive molecular dynamics (MD) simulations in the middle level to obtain the chemical reaction rates and equations of states. At the up lever, a smooth particle hydrodynamics (SPH) method incorporated ignition and growth model and afterburning model has been used for the simulation of the detonation and combustion of the aluminized explosive. Simulation is compared with experiment and good agreement is observed. The proposed multiscale method of SPH-MD-QM could be used to optimize the performance of aluminized explosives. The authors would like to acknowledge the generous financial support from the Defense Threat Reduction Agency (DTRA) Grant No. HDTRA1-13-1-0025 and the Office of Naval Research Grants ONR Award No. N00014-08-1-0462 and No. N00014-12-1-0527.

Simulation of drop movement over an inclined surface using smoothed particle hydrodynamics.

PubMed

Das, Arup K; Das, Prasanta K

2009-10-06

Smoothed particle hydrodynamics (SPH) is used to numerically simulate the movement of drops down an inclined plane. Diffuse interfaces have been assumed for tracking the motion of the contact line. The asymmetric shape of the three-dimensional drop and the variation of contact angle along its periphery can be calculated using the simulation. During the motion of a liquid drop down an inclined plane, an internal circulation of liquid particles is observed due to gravitational pull which causes periodic change in the drop shape. The critical angle of inclination required for the inception of drop motion is also evaluated for different fluids as a function of drop volume. The numerical predictions exhibit a good agreement with the published experimental results.

SPH-DEM approach to numerically simulate the deformation of three-dimensional RBCs in non-uniform capillaries.

PubMed

Polwaththe-Gallage, Hasitha-Nayanajith; Saha, Suvash C; Sauret, Emilie; Flower, Robert; Senadeera, Wijitha; Gu, YuanTong

2016-12-28

Blood continuously flows through the blood vessels in the human body. When blood flows through the smallest blood vessels, red blood cells (RBCs) in the blood exhibit various types of motion and deformed shapes. Computational modelling techniques can be used to successfully predict the behaviour of the RBCs in capillaries. In this study, we report the application of a meshfree particle approach to model and predict the motion and deformation of three-dimensional RBCs in capillaries. An elastic spring network based on the discrete element method (DEM) is employed to model the three-dimensional RBC membrane. The haemoglobin in the RBC and the plasma in the blood are modelled as smoothed particle hydrodynamics (SPH) particles. For validation purposes, the behaviour of a single RBC in a simple shear flow is examined and compared against experimental results. Then simulations are carried out to predict the behaviour of RBCs in a capillary; (i) the motion of five identical RBCs in a uniform capillary, (ii) the motion of five identical RBCs with different bending stiffness (K b ) values in a stenosed capillary, (iii) the motion of three RBCs in a narrow capillary. Finally five identical RBCs are employed to determine the critical diameter of a stenosed capillary. Validation results showed a good agreement with less than 10% difference. From the above simulations, the following results are obtained; (i) RBCs exhibit different deformation behaviours due to the hydrodynamic interaction between them. (ii) Asymmetrical deformation behaviours of the RBCs are clearly observed when the bending stiffness (K b ) of the RBCs is changed. (iii) The model predicts the ability of the RBCs to squeeze through smaller blood vessels. Finally, from the simulations, the critical diameter of the stenosed section to stop the motion of blood flow is predicted. A three-dimensional spring network model based on DEM in combination with the SPH method is successfully used to model the motion and

A Global Three-Dimensional Radiation Hydrodynamic Simulation of a Self-Gravitating Accretion Disk

NASA Astrophysics Data System (ADS)

Phillipson, Rebecca; Vogeley, Michael S.; McMillan, Stephen; Boyd, Patricia

2018-01-01

We present three-dimensional, radiation hydrodynamic simulations of initially thin accretion disks with self-gravity using the grid-based code PLUTO. We produce simulated light curves and spectral energy distributions and compare to observational data of X-ray binary (XRB) and active galactic nuclei (AGN) variability. These simulations are of interest for modeling the role of radiation in accretion physics across decades of mass and frequency. In particular, the characteristics of the time variability in various bandwidths can probe the timescales over which different physical processes dominate the accretion flow. For example, in the case of some XRBs, superorbital periods much longer than the companion orbital period have been observed. Smoothed particle hydrodynamics (SPH) calculations have shown that irradiation-driven warping could be the mechanism underlying these long periods. In the case of AGN, irradiation-driven warping is also predicted to occur in addition to strong outflows originating from thermal and radiation pressure driving forces, which are important processes in understanding feedback and star formation in active galaxies. We compare our simulations to various toy models via traditional time series analysis of our synthetic and observed light curves.

A shock-capturing SPH scheme based on adaptive kernel estimation

NASA Astrophysics Data System (ADS)

Sigalotti, Leonardo Di G.; López, Hender; Donoso, Arnaldo; Sira, Eloy; Klapp, Jaime

2006-02-01

Here we report a method that converts standard smoothed particle hydrodynamics (SPH) into a working shock-capturing scheme without relying on solutions to the Riemann problem. Unlike existing adaptive SPH simulations, the present scheme is based on an adaptive kernel estimation of the density, which combines intrinsic features of both the kernel and nearest neighbor approaches in a way that the amount of smoothing required in low-density regions is effectively controlled. Symmetrized SPH representations of the gas dynamic equations along with the usual kernel summation for the density are used to guarantee variational consistency. Implementation of the adaptive kernel estimation involves a very simple procedure and allows for a unique scheme that handles strong shocks and rarefactions the same way. Since it represents a general improvement of the integral interpolation on scattered data, it is also applicable to other fluid-dynamic models. When the method is applied to supersonic compressible flows with sharp discontinuities, as in the classical one-dimensional shock-tube problem and its variants, the accuracy of the results is comparable, and in most cases superior, to that obtained from high quality Godunov-type methods and SPH formulations based on Riemann solutions. The extension of the method to two- and three-space dimensions is straightforward. In particular, for the two-dimensional cylindrical Noh's shock implosion and Sedov point explosion problems the present scheme produces much better results than those obtained with conventional SPH codes.

Modeling and Simulation of Ceramic Arrays to Improve Ballistic Performance

DTIC Science & Technology

2014-01-17

30cal AP M2 Projectile, 762x39 PS Projectile, SPH , Aluminum 5083, SiC, DoP Expeminets, AutoDyn Simulations, Tile Gap 16. SECURITY CLASSIFICATION...particle hydrodynamics ( SPH ) is applied for all parts. The SPH particle size is .4 mm, with the assumption that modeling dust smaller than .4 mm can be

Direct collapse to supermassive black hole seeds: comparing the AMR and SPH approaches.

PubMed

Luo, Yang; Nagamine, Kentaro; Shlosman, Isaac

2016-07-01

We provide detailed comparison between the adaptive mesh refinement (AMR) code enzo-2.4 and the smoothed particle hydrodynamics (SPH)/ N -body code gadget-3 in the context of isolated or cosmological direct baryonic collapse within dark matter (DM) haloes to form supermassive black holes. Gas flow is examined by following evolution of basic parameters of accretion flows. Both codes show an overall agreement in the general features of the collapse; however, many subtle differences exist. For isolated models, the codes increase their spatial and mass resolutions at different pace, which leads to substantially earlier collapse in SPH than in AMR cases due to higher gravitational resolution in gadget-3. In cosmological runs, the AMR develops a slightly higher baryonic resolution than SPH during halo growth via cold accretion permeated by mergers. Still, both codes agree in the build-up of DM and baryonic structures. However, with the onset of collapse, this difference in mass and spatial resolution is amplified, so evolution of SPH models begins to lag behind. Such a delay can have effect on formation/destruction rate of H 2 due to UV background, and on basic properties of host haloes. Finally, isolated non-cosmological models in spinning haloes, with spin parameter λ ∼ 0.01-0.07, show delayed collapse for greater λ, but pace of this increase is faster for AMR. Within our simulation set-up, gadget-3 requires significantly larger computational resources than enzo-2.4 during collapse, and needs similar resources, during the pre-collapse, cosmological structure formation phase. Yet it benefits from substantially higher gravitational force and hydrodynamic resolutions, except at the end of collapse.

Direct collapse to supermassive black hole seeds: comparing the AMR and SPH approaches

NASA Astrophysics Data System (ADS)

Luo, Yang; Nagamine, Kentaro; Shlosman, Isaac

2016-07-01

We provide detailed comparison between the adaptive mesh refinement (AMR) code ENZO-2.4 and the smoothed particle hydrodynamics (SPH)/N-body code GADGET-3 in the context of isolated or cosmological direct baryonic collapse within dark matter (DM) haloes to form supermassive black holes. Gas flow is examined by following evolution of basic parameters of accretion flows. Both codes show an overall agreement in the general features of the collapse; however, many subtle differences exist. For isolated models, the codes increase their spatial and mass resolutions at different pace, which leads to substantially earlier collapse in SPH than in AMR cases due to higher gravitational resolution in GADGET-3. In cosmological runs, the AMR develops a slightly higher baryonic resolution than SPH during halo growth via cold accretion permeated by mergers. Still, both codes agree in the build-up of DM and baryonic structures. However, with the onset of collapse, this difference in mass and spatial resolution is amplified, so evolution of SPH models begins to lag behind. Such a delay can have effect on formation/destruction rate of H2 due to UV background, and on basic properties of host haloes. Finally, isolated non-cosmological models in spinning haloes, with spin parameter λ ˜ 0.01-0.07, show delayed collapse for greater λ, but pace of this increase is faster for AMR. Within our simulation set-up, GADGET-3 requires significantly larger computational resources than ENZO-2.4 during collapse, and needs similar resources, during the pre-collapse, cosmological structure formation phase. Yet it benefits from substantially higher gravitational force and hydrodynamic resolutions, except at the end of collapse.

Hydrodynamic Simulations of Giant Impacts

NASA Astrophysics Data System (ADS)

Reinhardt, Christian; Stadel, Joachim

2013-07-01

We studied the basic numerical aspects of giant impacts using Smoothed Particles Hydrodynamics (SPH), which has been used in most of the prior studies conducted in this area (e.g., Benz, Canup). Our main goal was to modify the massive parallel, multi-stepping code GASOLINE widely used in cosmological simulations so that it can properly simulate the behavior of condensed materials such as granite or iron using the Tillotson equation of state. GASOLINE has been used to simulate hundreds of millions of particles for ideal gas physics so that using several millions of particles in condensed material simulations seems possible. In order to focus our attention of the numerical aspects of the problem we neglected the internal structure of the protoplanets and modelled them as homogenous (isothermal) granite spheres. For the energy balance we only considered PdV work and shock heating of the material during the impact (neglected cooling of the material). Starting at a low resolution of 2048 particles for the target and the impactor we run several simulations for different impact parameters and impact velocities and successfully reproduced the main features of the pioneering work of Benz from 1986. The impact sends a shock wave through both bodies heating the target and disrupting the remaining impactor. As in prior simulations material is ejected from the collision. How much, and whether it leaves the system or survives in an orbit for a longer time, depends on the initial conditions but also on resolution. Increasing the resolution (to 1.2x10⁶ particles) results in both a much clearer shock wave and deformation of the bodies during the impact and a more compact and detailed "arm" like structure of the ejected material. Currently we are investigating some numerical issues we encountered and are implementing differentiated models, making one step closer to more realistic protoplanets in such giant impact simulations.

A Novel Method for Modeling Neumann and Robin Boundary Conditions in Smoothed Particle Hydrodynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ryan, Emily M.; Tartakovsky, Alexandre M.; Amon, Cristina

2010-08-26

In this paper we present an improved method for handling Neumann or Robin boundary conditions in smoothed particle hydrodynamics. The Neumann and Robin boundary conditions are common to many physical problems (such as heat/mass transfer), and can prove challenging to model in volumetric modeling techniques such as smoothed particle hydrodynamics (SPH). A new SPH method for diffusion type equations subject to Neumann or Robin boundary conditions is proposed. The new method is based on the continuum surface force model [1] and allows an efficient implementation of the Neumann and Robin boundary conditions in the SPH method for geometrically complex boundaries.more » The paper discusses the details of the method and the criteria needed to apply the model. The model is used to simulate diffusion and surface reactions and its accuracy is demonstrated through test cases for boundary conditions describing different surface reactions.« less

Comparison of ALE and SPH Simulations of Vertical Drop Tests of a Composite Fuselage Section into Water

NASA Technical Reports Server (NTRS)

Jackson, Karen E.; Fuchs, Yvonne T.

2008-01-01

Simulation of multi-terrain impact has been identified as an important research area for improved prediction of rotorcraft crashworthiness within the NASA Subsonic Rotary Wing Aeronautics Program on Rotorcraft Crashworthiness. As part of this effort, two vertical drop tests were conducted of a 5-ft-diameter composite fuselage section into water. For the first test, the fuselage section was impacted in a baseline configuration without energy absorbers. For the second test, the fuselage section was retrofitted with a composite honeycomb energy absorber. Both tests were conducted at a nominal velocity of 25-ft/s. A detailed finite element model was developed to represent each test article and water impact was simulated using both Arbitrary Lagrangian Eulerian (ALE) and Smooth Particle Hydrodynamics (SPH) approaches in LS-DYNA, a nonlinear, explicit transient dynamic finite element code. Analytical predictions were correlated with experimental data for both test configurations. In addition, studies were performed to evaluate the influence of mesh density on test-analysis correlation.

Development and initial validation of a novel smoothed-particle hydrodynamics-based simulation model of trabecular bone penetration by metallic implants.

PubMed

Kulper, Sloan A; Fang, Christian X; Ren, Xiaodan; Guo, Margaret; Sze, Kam Y; Leung, Frankie K L; Lu, William W

2018-04-01

A novel computational model of implant migration in trabecular bone was developed using smoothed-particle hydrodynamics (SPH), and an initial validation was performed via correlation with experimental data. Six fresh-frozen human cadaveric specimens measuring 10 × 10 × 20 mm were extracted from the proximal femurs of female donors (mean age of 82 years, range 75-90, BV/TV ratios between 17.88% and 30.49%). These specimens were then penetrated under axial loading to a depth of 10 mm with 5 mm diameter cylindrical indenters bearing either flat or sharp/conical tip designs similar to blunt and self-tapping cancellous screws, assigned in a random manner. SPH models were constructed based on microCT scans (17.33 µm) of the cadaveric specimens. Two initial specimens were used for calibration of material model parameters. The remaining four specimens were then simulated in silico using identical material model parameters. Peak forces varied between 92.0 and 365.0 N in the experiments, and 115.5-352.2 N in the SPH simulations. The concordance correlation coefficient between experimental and simulated pairs was 0.888, with a 95%CI of 0.8832-0.8926, a Pearson ρ (precision) value of 0.9396, and a bias correction factor Cb (accuracy) value of 0.945. Patterns of bone compaction were qualitatively similar; both experimental and simulated flat-tipped indenters produced dense regions of compacted material adjacent to the advancing face of the indenter, while sharp-tipped indenters deposited compacted material along their peripheries. Simulations based on SPH can produce accurate predictions of trabecular bone penetration that are useful for characterizing implant performance under high-strain loading conditions. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:1114-1123, 2018. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

Smoothed particle hydrodynamics simulations of black hole accretion: a step to model black hole feedback in galaxies

NASA Astrophysics Data System (ADS)

Barai, Paramita; Proga, Daniel; Nagamine, Kentaro

2011-11-01

We test how accurately the smoothed particle hydrodynamics (SPH) numerical technique can follow spherically symmetric Bondi accretion. Using the 3D SPH code GADGET-3, we perform simulations of gas accretion on to a central supermassive black hole of mass 108 M⊙ within the radial range of 0.1-200 pc. We carry out simulations without and with radiative heating by a central X-ray corona and radiative cooling. For an adiabatic case, the radial profiles of hydrodynamical properties match the Bondi solution, except near the inner and outer radius of the computational domain. The deviation from the Bondi solution close to the inner radius is caused by the combination of numerical resolution, artificial viscosity and our inner boundary condition. Near the outer radius (≤200 pc), we observe either an outflow or development of a non-spherical inflow unless the outer boundary conditions are very stringently implemented. Despite these issues related to the boundary conditions, we find that adiabatic Bondi accretion can be reproduced for durations of a few dynamical times at the Bondi radius, and for longer times if the outer radius is increased. In particular, the mass inflow rate at the inner boundary, which we measure, is within 3-4 per cent of the Bondi accretion rate. With radiative heating and cooling included, the spherically accreting gas takes a longer time to reach a steady state than the adiabatic Bondi accretion runs, and in some cases does not reach a steady state even within several hundred dynamical times. We find that artificial viscosity causes excessive heating near the inner radius, making the thermal properties of the gas inconsistent with a physical solution. This overheating occurs typically only in the supersonic part of the flow, so that it does not affect the mass accretion rate. We see that increasing the X-ray luminosity produces a lower central mass inflow rate, implying that feedback due to radiative heating is operational in our simulations

Fast and accurate Voronoi density gridding from Lagrangian hydrodynamics data

NASA Astrophysics Data System (ADS)

Petkova, Maya A.; Laibe, Guillaume; Bonnell, Ian A.

2018-01-01

Voronoi grids have been successfully used to represent density structures of gas in astronomical hydrodynamics simulations. While some codes are explicitly built around using a Voronoi grid, others, such as Smoothed Particle Hydrodynamics (SPH), use particle-based representations and can benefit from constructing a Voronoi grid for post-processing their output. So far, calculating the density of each Voronoi cell from SPH data has been done numerically, which is both slow and potentially inaccurate. This paper proposes an alternative analytic method, which is fast and accurate. We derive an expression for the integral of a cubic spline kernel over the volume of a Voronoi cell and link it to the density of the cell. Mass conservation is ensured rigorously by the procedure. The method can be applied more broadly to integrate a spherically symmetric polynomial function over the volume of a random polyhedron.

SPH modelling of energy partitioning during impacts on Venus

NASA Technical Reports Server (NTRS)

Takata, T.; Ahrens, T. J.

1993-01-01

Impact cratering of the Venusian planetary surface by meteorites was investigated numerically using the Smoothed Particle Hydrodynamics (SPH) method. Venus presently has a dense atmosphere. Vigorous transfer of energy between impacting meteorites, the planetary surface, and the atmosphere is expected during impact events. The investigation concentrated on the effects of the atmosphere on energy partitioning and the flow of ejecta and gas. The SPH method is particularly suitable for studying complex motion, especially because of its ability to be extended to three dimensions. In our simulations, particles representing impactors and targets are initially set to a uniform density, and those of atmosphere are set to be in hydrostatic equilibrium. Target, impactor, and atmosphere are represented by 9800, 80, and 4200 particles, respectively. A Tillotson equation of state for granite is assumed for the target and impactor, and an ideal gas with constant specific heat ratio is used for the atmosphere. Two dimensional axisymmetric geometry was assumed and normal impacts of 10km diameter projectiles with velocities of 5, 10, 20, and 40 km/s, both with and without an atmosphere present were modeled.

Simulations of dolphin kick swimming using smoothed particle hydrodynamics.

PubMed

Cohen, Raymond C Z; Cleary, Paul W; Mason, Bruce R

2012-06-01

In competitive human swimming the submerged dolphin kick stroke (underwater undulatory swimming) is utilized after dives and turns. The optimal dolphin kick has a balance between minimizing drag and maximizing thrust while also minimizing the physical exertion required of the swimmer. In this study laser scans of athletes are used to provide realistic swimmer geometries in a single anatomical pose. These are rigged and animated to closely match side-on video footage. Smoothed Particle Hydrodynamics (SPH) fluid simulations are performed to evaluate variants of this swimming stroke technique. This computational approach provides full temporal and spatial information about the flow moving around the deforming swimmer model. The effects of changes in ankle flexibility and stroke frequency are investigated through a parametric study. The results suggest that the net streamwise force on the swimmer is relatively insensitive to ankle flexibility but is strongly dependent on kick frequency. Crown Copyright © 2011. Published by Elsevier B.V. All rights reserved.

A generalized transport-velocity formulation for smoothed particle hydrodynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Chi; Hu, Xiangyu Y., E-mail: xiangyu.hu@tum.de; Adams, Nikolaus A.

The standard smoothed particle hydrodynamics (SPH) method suffers from tensile instability. In fluid-dynamics simulations this instability leads to particle clumping and void regions when negative pressure occurs. In solid-dynamics simulations, it results in unphysical structure fragmentation. In this work the transport-velocity formulation of Adami et al. (2013) is generalized for providing a solution of this long-standing problem. Other than imposing a global background pressure, a variable background pressure is used to modify the particle transport velocity and eliminate the tensile instability completely. Furthermore, such a modification is localized by defining a shortened smoothing length. The generalized formulation is suitable formore » fluid and solid materials with and without free surfaces. The results of extensive numerical tests on both fluid and solid dynamics problems indicate that the new method provides a unified approach for multi-physics SPH simulations.« less

Neptune: An astrophysical smooth particle hydrodynamics code for massively parallel computer architectures

NASA Astrophysics Data System (ADS)

Sandalski, Stou

Smooth particle hydrodynamics is an efficient method for modeling the dynamics of fluids. It is commonly used to simulate astrophysical processes such as binary mergers. We present a newly developed GPU accelerated smooth particle hydrodynamics code for astrophysical simulations. The code is named neptune after the Roman god of water. It is written in OpenMP parallelized C++ and OpenCL and includes octree based hydrodynamic and gravitational acceleration. The design relies on object-oriented methodologies in order to provide a flexible and modular framework that can be easily extended and modified by the user. Several pre-built scenarios for simulating collisions of polytropes and black-hole accretion are provided. The code is released under the MIT Open Source license and publicly available at http://code.google.com/p/neptune-sph/.

Neighbour lists for smoothed particle hydrodynamics on GPUs

NASA Astrophysics Data System (ADS)

Winkler, Daniel; Rezavand, Massoud; Rauch, Wolfgang

2018-04-01

The efficient iteration of neighbouring particles is a performance critical aspect of any high performance smoothed particle hydrodynamics (SPH) solver. SPH solvers that implement a constant smoothing length generally divide the simulation domain into a uniform grid to reduce the computational complexity of the neighbour search. Based on this method, particle neighbours are either stored per grid cell or for each individual particle, denoted as Verlet list. While the latter approach has significantly higher memory requirements, it has the potential for a significant computational speedup. A theoretical comparison is performed to estimate the potential improvements of the method based on unknown hardware dependent factors. Subsequently, the computational performance of both approaches is empirically evaluated on graphics processing units. It is shown that the speedup differs significantly for different hardware, dimensionality and floating point precision. The Verlet list algorithm is implemented as an alternative to the cell linked list approach in the open-source SPH solver DualSPHysics and provided as a standalone software package.

Numerical simulation of wave-current interaction using the SPH method

NASA Astrophysics Data System (ADS)

He, Ming; Gao, Xi-feng; Xu, Wan-hai

2018-05-01

In this paper, the smoothed particle hydrodynamics (SPH) method is used to build a numerical wave-current tank (NWCT). The wave is generated by using a piston-type wave generator and is absorbed by using a sponge layer. The uniform current field is generated by simultaneously imposing the directional velocity and hydrostatic pressure in both inflow and outflow regions set below the NWCT. Particle cyclic boundaries are also implemented for recycling the Lagrangian fluid particles. Furthermore, to shorten the time to reach a steady state, a temporary rigid-lid treatment for the water surface is proposed. It turns out to be very effective for weakening the undesired oscillatory flow at the beginning stage of the current generation. The calculated water surface elevation and horizontal-velocity profile are validated against the available experimental data. Satisfactory agreements are obtained, demonstrating the good capability of the NWCT.

SWIFT: SPH With Inter-dependent Fine-grained Tasking

NASA Astrophysics Data System (ADS)

Schaller, Matthieu; Gonnet, Pedro; Chalk, Aidan B. G.; Draper, Peter W.

2018-05-01

SWIFT runs cosmological simulations on peta-scale machines for solving gravity and SPH. It uses the Fast Multipole Method (FMM) to calculate gravitational forces between nearby particles, combining these with long-range forces provided by a mesh that captures both the periodic nature of the calculation and the expansion of the simulated universe. SWIFT currently uses a single fixed but time-variable softening length for all the particles. Many useful external potentials are also available, such as galaxy haloes or stratified boxes that are used in idealised problems. SWIFT implements a standard LCDM cosmology background expansion and solves the equations in a comoving frame; equations of state of dark-energy evolve with scale-factor. The structure of the code allows implementation for modified-gravity solvers or self-interacting dark matter schemes to be implemented. Many hydrodynamics schemes are implemented in SWIFT and the software allows users to add their own.

ALARIC: An algorithm for constructing arbitrarily complex initial density distributions with low particle noise for SPH/SPMHD applications

NASA Astrophysics Data System (ADS)

Vela Vela, Luis; Sanchez, Raul; Geiger, Joachim

2018-03-01

A method is presented to obtain initial conditions for Smoothed Particle Hydrodynamic (SPH) scenarios where arbitrarily complex density distributions and low particle noise are needed. Our method, named ALARIC, tampers with the evolution of the internal variables to obtain a fast and efficient profile evolution towards the desired goal. The result has very low levels of particle noise and constitutes a perfect candidate to study the equilibrium and stability properties of SPH/SPMHD systems. The method uses the iso-thermal SPH equations to calculate hydrodynamical forces under the presence of an external fictitious potential and evolves them in time with a 2nd-order symplectic integrator. The proposed method generates tailored initial conditions that perform better in many cases than those based on purely crystalline lattices, since it prevents the appearance of anisotropies.

CRKSPH: A new meshfree hydrodynamics method with applications to astrophysics

NASA Astrophysics Data System (ADS)

Owen, John Michael; Raskin, Cody; Frontiere, Nicholas

2018-01-01

The study of astrophysical phenomena such as supernovae, accretion disks, galaxy formation, and large-scale structure formation requires computational modeling of, at a minimum, hydrodynamics and gravity. Developing numerical methods appropriate for these kinds of problems requires a number of properties: shock-capturing hydrodynamics benefits from rigorous conservation of invariants such as total energy, linear momentum, and mass; lack of obvious symmetries or a simplified spatial geometry to exploit necessitate 3D methods that ideally are Galilean invariant; the dynamic range of mass and spatial scales that need to be resolved can span many orders of magnitude, requiring methods that are highly adaptable in their space and time resolution. We have developed a new Lagrangian meshfree hydrodynamics method called Conservative Reproducing Kernel Smoothed Particle Hydrodynamics, or CRKSPH, in order to meet these goals. CRKSPH is a conservative generalization of the meshfree reproducing kernel method, combining the high-order accuracy of reproducing kernels with the explicit conservation of mass, linear momentum, and energy necessary to study shock-driven hydrodynamics in compressible fluids. CRKSPH's Lagrangian, particle-like nature makes it simple to combine with well-known N-body methods for modeling gravitation, similar to the older Smoothed Particle Hydrodynamics (SPH) method. Indeed, CRKSPH can be substituted for SPH in existing SPH codes due to these similarities. In comparison to SPH, CRKSPH is able to achieve substantially higher accuracy for a given number of points due to the explicitly consistent (and higher-order) interpolation theory of reproducing kernels, while maintaining the same conservation principles (and therefore applicability) as SPH. There are currently two coded implementations of CRKSPH available: one in the open-source research code Spheral, and the other in the high-performance cosmological code HACC. Using these codes we have applied

A new approach to fluid-structure interaction within graphics hardware accelerated smooth particle hydrodynamics considering heterogeneous particle size distribution

NASA Astrophysics Data System (ADS)

Eghtesad, Adnan; Knezevic, Marko

2018-07-01

A corrective smooth particle method (CSPM) within smooth particle hydrodynamics (SPH) is used to study the deformation of an aircraft structure under high-velocity water-ditching impact load. The CSPM-SPH method features a new approach for the prediction of two-way fluid-structure interaction coupling. Results indicate that the implementation is well suited for modeling the deformation of structures under high-velocity impact into water as evident from the predicted stress and strain localizations in the aircraft structure as well as the integrity of the impacted interfaces, which show no artificial particle penetrations. To reduce the simulation time, a heterogeneous particle size distribution over a complex three-dimensional geometry is used. The variable particle size is achieved from a finite element mesh with variable element size and, as a result, variable nodal (i.e., SPH particle) spacing. To further accelerate the simulations, the SPH code is ported to a graphics processing unit using the OpenACC standard. The implementation and simulation results are described and discussed in this paper.

A new approach to fluid-structure interaction within graphics hardware accelerated smooth particle hydrodynamics considering heterogeneous particle size distribution

NASA Astrophysics Data System (ADS)

Eghtesad, Adnan; Knezevic, Marko

2017-12-01

A corrective smooth particle method (CSPM) within smooth particle hydrodynamics (SPH) is used to study the deformation of an aircraft structure under high-velocity water-ditching impact load. The CSPM-SPH method features a new approach for the prediction of two-way fluid-structure interaction coupling. Results indicate that the implementation is well suited for modeling the deformation of structures under high-velocity impact into water as evident from the predicted stress and strain localizations in the aircraft structure as well as the integrity of the impacted interfaces, which show no artificial particle penetrations. To reduce the simulation time, a heterogeneous particle size distribution over a complex three-dimensional geometry is used. The variable particle size is achieved from a finite element mesh with variable element size and, as a result, variable nodal (i.e., SPH particle) spacing. To further accelerate the simulations, the SPH code is ported to a graphics processing unit using the OpenACC standard. The implementation and simulation results are described and discussed in this paper.

Numerical simulation of hemorrhage in human injury

NASA Astrophysics Data System (ADS)

Chong, Kwitae; Jiang, Chenfanfu; Santhanam, Anand; Benharash, Peyman; Teran, Joseph; Eldredge, Jeff

2015-11-01

Smoothed Particle Hydrodynamics (SPH) is adapted to simulate hemorrhage in the injured human body. As a Lagrangian fluid simulation, SPH uses fluid particles as computational elements and thus mass conservation is trivially satisfied. In order to ensure anatomical fidelity, a three-dimensional reconstruction of a portion of the human body -here, demonstrated on the lower leg- is sampled as skin, bone and internal tissue particles from the CT scan image of an actual patient. The injured geometry is then generated by simulation of ballistic projectiles passing through the anatomical model with the Material Point Method (MPM) and injured vessel segments are identified. From each such injured segment, SPH is used to simulate bleeding, with inflow boundary condition obtained from a coupled 1-d vascular tree model. Blood particles interact with impermeable bone and skin particles through the Navier-Stokes equations and with permeable internal tissue particles through the Brinkman equations. The SPH results are rendered in post-processing for improved visual fidelity. The overall simulation strategy is demonstrated on several injury scenarios in the lower leg.

Enforcing dust mass conservation in 3D simulations of tightly coupled grains with the PHANTOM SPH code

NASA Astrophysics Data System (ADS)

Ballabio, G.; Dipierro, G.; Veronesi, B.; Lodato, G.; Hutchison, M.; Laibe, G.; Price, D. J.

2018-06-01

We describe a new implementation of the one-fluid method in the SPH code PHANTOM to simulate the dynamics of dust grains in gas protoplanetary discs. We revise and extend previously developed algorithms by computing the evolution of a new fluid quantity that produces a more accurate and numerically controlled evolution of the dust dynamics. Moreover, by limiting the stopping time of uncoupled grains that violate the assumptions of the terminal velocity approximation, we avoid fatal numerical errors in mass conservation. We test and validate our new algorithm by running 3D SPH simulations of a large range of disc models with tightly and marginally coupled grains.

A smooth particle hydrodynamics code to model collisions between solid, self-gravitating objects

NASA Astrophysics Data System (ADS)

Schäfer, C.; Riecker, S.; Maindl, T. I.; Speith, R.; Scherrer, S.; Kley, W.

2016-05-01

Context. Modern graphics processing units (GPUs) lead to a major increase in the performance of the computation of astrophysical simulations. Owing to the different nature of GPU architecture compared to traditional central processing units (CPUs) such as x86 architecture, existing numerical codes cannot be easily migrated to run on GPU. Here, we present a new implementation of the numerical method smooth particle hydrodynamics (SPH) using CUDA and the first astrophysical application of the new code: the collision between Ceres-sized objects. Aims: The new code allows for a tremendous increase in speed of astrophysical simulations with SPH and self-gravity at low costs for new hardware. Methods: We have implemented the SPH equations to model gas, liquids and elastic, and plastic solid bodies and added a fragmentation model for brittle materials. Self-gravity may be optionally included in the simulations and is treated by the use of a Barnes-Hut tree. Results: We find an impressive performance gain using NVIDIA consumer devices compared to our existing OpenMP code. The new code is freely available to the community upon request. If you are interested in our CUDA SPH code miluphCUDA, please write an email to Christoph Schäfer. miluphCUDA is the CUDA port of miluph. miluph is pronounced [maßl2v]. We do not support the use of the code for military purposes.

Landslides and tsunamis predicted by incompressible smoothed particle hydrodynamics (SPH) with application to the 1958 Lituya Bay event and idealized experiment.

PubMed

Xenakis, A M; Lind, S J; Stansby, P K; Rogers, B D

2017-03-01

Tsunamis caused by landslides may result in significant destruction of the surroundings with both societal and industrial impact. The 1958 Lituya Bay landslide and tsunami is a recent and well-documented terrestrial landslide generating a tsunami with a run-up of 524 m. Although recent computational techniques have shown good performance in the estimation of the run-up height, they fail to capture all the physical processes, in particular, the landslide-entry profile and interaction with the water. Smoothed particle hydrodynamics (SPH) is a versatile numerical technique for describing free-surface and multi-phase flows, particularly those that exhibit highly nonlinear deformation in landslide-generated tsunamis. In the current work, the novel multi-phase incompressible SPH method with shifting is applied to the Lituya Bay tsunami and landslide and is the first methodology able to reproduce realistically both the run-up and landslide-entry as documented in a benchmark experiment. The method is the first paper to develop a realistic implementation of the physics that in addition to the non-Newtonian rheology of the landslide includes turbulence in the water phase and soil saturation. Sensitivity to the experimental initial conditions is also considered. This work demonstrates the ability of the proposed method in modelling challenging environmental multi-phase, non-Newtonian and turbulent flows.

Smoothed Particle Hydrodynamics and its applications for multiphase flow and reactive transport in porous media

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tartakovsky, Alexandre M.; Trask, Nathaniel; Pan, K.

2016-03-11

Smoothed Particle Hydrodynamics (SPH) is a Lagrangian method based on a meshless discretization of partial differential equations. In this review, we present SPH discretization of the Navier-Stokes and Advection-Diffusion-Reaction equations, implementation of various boundary conditions, and time integration of the SPH equations, and we discuss applications of the SPH method for modeling pore-scale multiphase flows and reactive transport in porous and fractured media.

GPUs, a New Tool of Acceleration in CFD: Efficiency and Reliability on Smoothed Particle Hydrodynamics Methods

PubMed Central

Crespo, Alejandro C.; Dominguez, Jose M.; Barreiro, Anxo; Gómez-Gesteira, Moncho; Rogers, Benedict D.

2011-01-01

Smoothed Particle Hydrodynamics (SPH) is a numerical method commonly used in Computational Fluid Dynamics (CFD) to simulate complex free-surface flows. Simulations with this mesh-free particle method far exceed the capacity of a single processor. In this paper, as part of a dual-functioning code for either central processing units (CPUs) or Graphics Processor Units (GPUs), a parallelisation using GPUs is presented. The GPU parallelisation technique uses the Compute Unified Device Architecture (CUDA) of nVidia devices. Simulations with more than one million particles on a single GPU card exhibit speedups of up to two orders of magnitude over using a single-core CPU. It is demonstrated that the code achieves different speedups with different CUDA-enabled GPUs. The numerical behaviour of the SPH code is validated with a standard benchmark test case of dam break flow impacting on an obstacle where good agreement with the experimental results is observed. Both the achieved speed-ups and the quantitative agreement with experiments suggest that CUDA-based GPU programming can be used in SPH methods with efficiency and reliability. PMID:21695185

Numerical Viscosity and the Survival of Gas Giant Protoplanets in Disk Simulations

NASA Astrophysics Data System (ADS)

Pickett, Megan K.; Durisen, Richard H.

2007-01-01

We present three-dimensional hydrodynamic simulations of a gravitationally unstable protoplanetary disk model under the condition of local isothermality. Ordinarily, local isothermality precludes the need for an artificial viscosity (AV) scheme to mediate shocks. Without AV, the disk evolves violently, shredding into dense (although short-lived) clumps. When we introduce our AV treatment in the momentum equation, but without heating due to irreversible compression, our grid-based simulations begin to resemble smoothed particle hydrodynamics (SPH) calculations, where clumps are more likely to survive many orbits. In fact, the standard SPH viscosity appears comparable in strength to the AV that leads to clump longevity in our code. This sensitivity to one numerical parameter suggests extreme caution in interpreting simulations by any code in which long-lived gaseous protoplanetary bodies appear.

SPH modeling of the Stickney impact at Phobos

NASA Astrophysics Data System (ADS)

Bruck Syal, Megan; Rovny, Jared; Owen, J. Michael; Miller, Paul L.

2016-10-01

Stickney crater stretches across nearly half the diameter of ~22-km Phobos, the larger of the two martian moons. The Stickney-forming impact would have had global consequences for Phobos, causing extensive damage to the satellite's interior and initiating large-scale resurfacing through ejecta blanket emplacement. Further, much of the ejected material that initially escaped the moon's tiny gravity (escape velocity of ~11 m/s) would have likely reimpacted on subsequent orbits. Modeling of the impact event is necessary to understand the conditions that allowed this "megacrater" to form without disrupting the entire satellite. Impact simulation results also provide a means to test several different hypotheses for how the mysterious families of parallel grooves may have formed at Phobos.We report on adaptive SPH simulations that successfully generate Stickney while avoiding catastrophic fragmentation of Phobos. Inclusion of target porosity and using sufficient numerical resolution in fully 3-D simulations are key for avoiding over-estimation of target damage. Cratering efficiency follows gravity-dominated scaling laws over a wide range of velocities (6-20 km/s) for the appropriate material constants. While the adaptive SPH results are used to constrain crater volume and fracture patterns within the target, additional questions about the fate of ejecta and final crater morphology within an unusual gravity environment can be addressed with complementary numerical methods. Results from the end of the hydrodynamics-controlled phase (tens of seconds after impact) are linked to a Discrete Element Method code, which can explore these processes over longer time scales (see Schwartz et al., this meeting).This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LLNL-ABS-695442.

Modeling Strain Rate Effect of Heterogeneous Materials Using SPH Method

NASA Astrophysics Data System (ADS)

Ma, G. W.; Wang, X. J.; Li, Q. M.

2010-11-01

The strain rate effect on the dynamic compressive failure of heterogeneous material based on the smoothed particle hydrodynamics (SPH) method is studied. The SPH method employs a rate-insensitive elasto-plastic damage model incorporated with a Weibull distribution law to reflect the mechanical behavior of heterogeneous rock-like materials. A series of simulations are performed for heterogeneous specimens by applying axial velocity conditions, which induce different strain-rate loadings to the specimen. A detailed failure process of the specimens in terms of microscopic crack-activities and the macro-mechanical response are discussed. Failure mechanisms between the low and high strain rate cases are compared. The result shows that the strain-rate effects on the rock strength are mainly caused by the changing internal pressure due to the inertial effects as well as the material heterogeneity. It also demonstrates that the inertial effect becomes significant only when the induced strain rate exceeds a threshold, below which, the dynamic strength enhancement can be explained due to the heterogeneities in the material. It also shows that the dynamic strength is affected more significantly for a relatively more heterogeneous specimen, which coincides with the experimental results showing that the poor quality specimen had a relatively larger increase in the dynamic strength.

Landslides and tsunamis predicted by incompressible smoothed particle hydrodynamics (SPH) with application to the 1958 Lituya Bay event and idealized experiment

PubMed Central

Lind, S. J.; Stansby, P. K.; Rogers, B. D.

2017-01-01

Tsunamis caused by landslides may result in significant destruction of the surroundings with both societal and industrial impact. The 1958 Lituya Bay landslide and tsunami is a recent and well-documented terrestrial landslide generating a tsunami with a run-up of 524 m. Although recent computational techniques have shown good performance in the estimation of the run-up height, they fail to capture all the physical processes, in particular, the landslide-entry profile and interaction with the water. Smoothed particle hydrodynamics (SPH) is a versatile numerical technique for describing free-surface and multi-phase flows, particularly those that exhibit highly nonlinear deformation in landslide-generated tsunamis. In the current work, the novel multi-phase incompressible SPH method with shifting is applied to the Lituya Bay tsunami and landslide and is the first methodology able to reproduce realistically both the run-up and landslide-entry as documented in a benchmark experiment. The method is the first paper to develop a realistic implementation of the physics that in addition to the non-Newtonian rheology of the landslide includes turbulence in the water phase and soil saturation. Sensitivity to the experimental initial conditions is also considered. This work demonstrates the ability of the proposed method in modelling challenging environmental multi-phase, non-Newtonian and turbulent flows. PMID:28413334

A smoothed particle hydrodynamics model for miscible flow in three-dimensional fractures and the two-dimensional Rayleigh–Taylor instability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tartakovsky, Alexandre M.; Meakin, Paul

2005-08-10

A numerical model based on smoothed particle hydrodynamics (SPH) has been developed and used to simulate the classical two-dimensional Rayleigh–Taylor instability and three-dimensional miscible flow in fracture apertures with complex geometries. To model miscible flow fluid particles with variable, composition dependent, masses were used. By basing the SPH equations on the particle number density artificial surface tension effects were avoided. The simulation results for the growth of a single perturbation driven by the Rayleigh – Taylor instability compare well with numerical results obtained by Fournier et al., and the growth of a perturbation with time can be represented quite wellmore » by a second-degree polynomial, in accord with the linear stability analysis of Duff et al. The dispersion coefficient found from SPH simulation of flow and diffusion in an ideal fracture was in excellent agreement with the value predicted by the theory of Taylor and Aris. The simulations of miscible flow in fracture apertures can be used to determination dispersion coefficients for transport in fractured media - a parameter used in large-scale simulations of contaminant transport.« less

Coupled SPH-FV method with net vorticity and mass transfer

NASA Astrophysics Data System (ADS)

Chiron, L.; Marrone, S.; Di Mascio, A.; Le Touzé, D.

2018-07-01

Recently, an algorithm for coupling a Finite Volume (FV) method, that discretize the Navier-Stokes equations on block structured Eulerian grids, with the weakly-compressible Lagrangian Smoothed Particle Hydrodynamics (SPH) was presented in [16]. The algorithm takes advantage of the SPH method to discretize flow regions close to free-surfaces and of the FV method to resolve the bulk flow and the wall regions. The continuity between the two solutions is guaranteed by overlapping zones. Here we extend the algorithm by adding the possibility to have: 1) net mass transfer between the SPH and FV sub-domains; 2) free-surface across the overlapping region. In this context, particle generation at common boundaries is required to prevent depletion or clustering of particles. This operation is not trivial, because consistency between the Lagrangian and Eulerian description of the flow must be retained to ensure mass conservation. We propose here a new coupling paradigm that extends the algorithm developed in [16] and renders it suitable to test cases where vorticity and free surface significantly pass from one domain to the other. On the SPH side, a novel technique for the creation/deletion of particle was developed. On the FV side, the information recovered from the SPH solver are exploited to improve free surface prediction in a fashion that resemble the Particle Level-Set algorithms. The combination of the two new features was tested and validated in a number of test cases where both vorticity and front evolution are important. Convergence and robustness of the algorithm are shown.

SPH numerical investigation of the characteristics of an oscillating hydraulic jump at an abrupt drop

NASA Astrophysics Data System (ADS)

De Padova, Diana; Mossa, Michele; Sibilla, Stefano

2018-02-01

This paper shows the results of the smooth particle hydrodynamics (SPH) modelling of the hydraulic jump at an abrupt drop, where the transition from supercritical to subcritical flow is characterised by several flow patterns depending upon the inflow and tailwater conditions. SPH simulations are obtained by a pseudo-compressible XSPH scheme with pressure smoothing; turbulent stresses are represented either by an algebraic mixing-length model, or by a two-equation k- ɛ model. The numerical model is applied to analyse the occurrence of oscillatory flow conditions between two different jump types characterised by quasi-periodic oscillation, and the results are compared with experiments performed at the hydraulics laboratory of Bari Technical University. The purpose of this paper is to obtain a deeper understanding of the physical features of a flow which is in general difficult to be reproduced numerically, owing to its unstable character: in particular, vorticity and turbulent kinetic energy fields, velocity, water depth and pressure spectra downstream of the jump, and velocity and pressure cross-correlations can be computed and analysed.

A comparison of cosmological hydrodynamic codes

NASA Technical Reports Server (NTRS)

Kang, Hyesung; Ostriker, Jeremiah P.; Cen, Renyue; Ryu, Dongsu; Hernquist, Lars; Evrard, August E.; Bryan, Greg L.; Norman, Michael L.

1994-01-01

We present a detailed comparison of the simulation results of various hydrodynamic codes. Starting with identical initial conditions based on the cold dark matter scenario for the growth of structure, with parameters h = 0.5 Omega = Omega(sub b) = 1, and sigma(sub 8) = 1, we integrate from redshift z = 20 to z = O to determine the physical state within a representative volume of size L(exp 3) where L = 64 h(exp -1) Mpc. Five indenpendent codes are compared: three of them Eulerian mesh-based and two variants of the smooth particle hydrodynamics 'SPH' Lagrangian approach. The Eulerian codes were run at N(exp 3) = (32(exp 3), 64(exp 3), 128(exp 3), and 256(exp 3)) cells, the SPH codes at N(exp 3) = 32(exp 3) and 64(exp 3) particles. Results were then rebinned to a 16(exp 3) grid with the exception that the rebinned data should converge, by all techniques, to a common and correct result as N approaches infinity. We find that global averages of various physical quantities do, as expected, tend to converge in the rebinned model, but that uncertainites in even primitive quantities such as (T), (rho(exp 2))(exp 1/2) persists at the 3%-17% level achieve comparable and satisfactory accuracy for comparable computer time in their treatment of the high-density, high-temeprature regions as measured in the rebinned data; the variance among the five codes (at highest resolution) for the mean temperature (as weighted by rho(exp 2) is only 4.5%. Examined at high resolution we suspect that the density resolution is better in the SPH codes and the thermal accuracy in low-density regions better in the Eulerian codes. In the low-density, low-temperature regions the SPH codes have poor accuracy due to statiscal effects, and the Jameson code gives the temperatures which are too high, due to overuse of artificial viscosity in these high Mach number regions. Overall the comparison allows us to better estimate errors; it points to ways of improving this current generation ofhydrodynamic

A smoothed particle hydrodynamics framework for modelling multiphase interactions at meso-scale

NASA Astrophysics Data System (ADS)

Li, Ling; Shen, Luming; Nguyen, Giang D.; El-Zein, Abbas; Maggi, Federico

2018-01-01

A smoothed particle hydrodynamics (SPH) framework is developed for modelling multiphase interactions at meso-scale, including the liquid-solid interaction induced deformation of the solid phase. With an inter-particle force formulation that mimics the inter-atomic force in molecular dynamics, the proposed framework includes the long-range attractions between particles, and more importantly, the short-range repulsive forces to avoid particle clustering and instability problems. Three-dimensional numerical studies have been conducted to demonstrate the capabilities of the proposed framework to quantitatively replicate the surface tension of water, to model the interactions between immiscible liquids and solid, and more importantly, to simultaneously model the deformation of solid and liquid induced by the multiphase interaction. By varying inter-particle potential magnitude, the proposed SPH framework has successfully simulated various wetting properties ranging from hydrophobic to hydrophilic surfaces. The simulation results demonstrate the potential of the proposed framework to genuinely study complex multiphase interactions in wet granular media.

Mine Blast Loading: Experiments and Simulations

DTIC Science & Technology

2010-04-01

plates by approximately 50%. We investigated the root cause for this discrepancy. The simulations calculate a turbulent-like flow field characterized...Toussaint [19] evaluated two numerical methods, Smooth Particle Hydrodynamics ( SPH ) and Arbitrary Lagrangian Eulerian (ALE), to simulate a mine blast on...That is, the mine blast products were not flowing along the solid plate boundary in the simulations as freely as they should. 6 In particular, the V

Smoothed particle hydrodynamics model for Landau-Lifshitz-Navier-Stokes and advection-diffusion equations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kordilla, Jannes, E-mail: jkordil@gwdg.de; Pan, Wenxiao, E-mail: Wenxiao.Pan@pnnl.gov; Tartakovsky, Alexandre, E-mail: alexandre.tartakovsky@pnnl.gov

2014-12-14

We propose a novel smoothed particle hydrodynamics (SPH) discretization of the fully coupled Landau-Lifshitz-Navier-Stokes (LLNS) and stochastic advection-diffusion equations. The accuracy of the SPH solution of the LLNS equations is demonstrated by comparing the scaling of velocity variance and the self-diffusion coefficient with kinetic temperature and particle mass obtained from the SPH simulations and analytical solutions. The spatial covariance of pressure and velocity fluctuations is found to be in a good agreement with theoretical models. To validate the accuracy of the SPH method for coupled LLNS and advection-diffusion equations, we simulate the interface between two miscible fluids. We study formationmore » of the so-called “giant fluctuations” of the front between light and heavy fluids with and without gravity, where the light fluid lies on the top of the heavy fluid. We find that the power spectra of the simulated concentration field are in good agreement with the experiments and analytical solutions. In the absence of gravity, the power spectra decay as the power −4 of the wavenumber—except for small wavenumbers that diverge from this power law behavior due to the effect of finite domain size. Gravity suppresses the fluctuations, resulting in much weaker dependence of the power spectra on the wavenumber. Finally, the model is used to study the effect of thermal fluctuation on the Rayleigh-Taylor instability, an unstable dynamics of the front between a heavy fluid overlaying a light fluid. The front dynamics is shown to agree well with the analytical solutions.« less

Smoothed particle hydrodynamics model for Landau-Lifshitz-Navier-Stokes and advection-diffusion equations.

PubMed

Kordilla, Jannes; Pan, Wenxiao; Tartakovsky, Alexandre

2014-12-14

We propose a novel smoothed particle hydrodynamics (SPH) discretization of the fully coupled Landau-Lifshitz-Navier-Stokes (LLNS) and stochastic advection-diffusion equations. The accuracy of the SPH solution of the LLNS equations is demonstrated by comparing the scaling of velocity variance and the self-diffusion coefficient with kinetic temperature and particle mass obtained from the SPH simulations and analytical solutions. The spatial covariance of pressure and velocity fluctuations is found to be in a good agreement with theoretical models. To validate the accuracy of the SPH method for coupled LLNS and advection-diffusion equations, we simulate the interface between two miscible fluids. We study formation of the so-called "giant fluctuations" of the front between light and heavy fluids with and without gravity, where the light fluid lies on the top of the heavy fluid. We find that the power spectra of the simulated concentration field are in good agreement with the experiments and analytical solutions. In the absence of gravity, the power spectra decay as the power -4 of the wavenumber-except for small wavenumbers that diverge from this power law behavior due to the effect of finite domain size. Gravity suppresses the fluctuations, resulting in much weaker dependence of the power spectra on the wavenumber. Finally, the model is used to study the effect of thermal fluctuation on the Rayleigh-Taylor instability, an unstable dynamics of the front between a heavy fluid overlaying a light fluid. The front dynamics is shown to agree well with the analytical solutions.

Smoothed particle hydrodynamics model for Landau-Lifshitz Navier-Stokes and advection-diffusion equations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kordilla, Jannes; Pan, Wenxiao; Tartakovsky, Alexandre M.

2014-12-14

We propose a novel Smoothed Particle Hydrodynamics (SPH) discretization of the fully-coupled Landau-Lifshitz-Navier-Stokes (LLNS) and advection-diffusion equations. The accuracy of the SPH solution of the LLNS equations is demonstrated by comparing the scaling of velocity variance and self-diffusion coefficient with kinetic temperature and particle mass obtained from the SPH simulations and analytical solutions. The spatial covariance of pressure and velocity fluctuations are found to be in a good agreement with theoretical models. To validate the accuracy of the SPH method for the coupled LLNS and advection-diffusion equations, we simulate the interface between two miscible fluids. We study the formation ofmore » the so-called giant fluctuations of the front between light and heavy fluids with and without gravity, where the light fluid lays on the top of the heavy fluid. We find that the power spectra of the simulated concentration field is in good agreement with the experiments and analytical solutions. In the absence of gravity the the power spectra decays as the power -4 of the wave number except for small wave numbers which diverge from this power law behavior due to the effect of finite domain size. Gravity suppresses the fluctuations resulting in the much weaker dependence of the power spectra on the wave number. Finally the model is used to study the effect of thermal fluctuation on the Rayleigh-Taylor instability, an unstable dynamics of the front between a heavy fluid overlying a light fluid. The front dynamics is shown to agree well with the analytical solutions.« less

GIZMO: Multi-method magneto-hydrodynamics+gravity code

NASA Astrophysics Data System (ADS)

Hopkins, Philip F.

2014-10-01

GIZMO is a flexible, multi-method magneto-hydrodynamics+gravity code that solves the hydrodynamic equations using a variety of different methods. It introduces new Lagrangian Godunov-type methods that allow solving the fluid equations with a moving particle distribution that is automatically adaptive in resolution and avoids the advection errors, angular momentum conservation errors, and excessive diffusion problems that seriously limit the applicability of “adaptive mesh” (AMR) codes, while simultaneously avoiding the low-order errors inherent to simpler methods like smoothed-particle hydrodynamics (SPH). GIZMO also allows the use of SPH either in “traditional” form or “modern” (more accurate) forms, or use of a mesh. Self-gravity is solved quickly with a BH-Tree (optionally a hybrid PM-Tree for periodic boundaries) and on-the-fly adaptive gravitational softenings. The code is descended from P-GADGET, itself descended from GADGET-2 (ascl:0003.001), and many of the naming conventions remain (for the sake of compatibility with the large library of GADGET work and analysis software).

Modeling electrokinetic flows by consistent implicit incompressible smoothed particle hydrodynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pan, Wenxiao; Kim, Kyungjoo; Perego, Mauro

2017-04-01

We present an efficient implicit incompressible smoothed particle hydrodynamics (I2SPH) discretization of Navier-Stokes, Poisson-Boltzmann, and advection-diffusion equations subject to Dirichlet or Robin boundary conditions. It is applied to model various two and three dimensional electrokinetic flows in simple or complex geometries. The I2SPH's accuracy and convergence are examined via comparison with analytical solutions, grid-based numerical solutions, or empirical models. The new method provides a framework to explore broader applications of SPH in microfluidics and complex fluids with charged objects, such as colloids and biomolecules, in arbitrary complex geometries.

Modeling electrokinetic flows by consistent implicit incompressible smoothed particle hydrodynamics

DOE PAGES

Pan, Wenxiao; Kim, Kyungjoo; Perego, Mauro; ...

2017-01-03

In this paper, we present a consistent implicit incompressible smoothed particle hydrodynamics (I 2SPH) discretization of Navier–Stokes, Poisson–Boltzmann, and advection–diffusion equations subject to Dirichlet or Robin boundary conditions. It is applied to model various two and three dimensional electrokinetic flows in simple or complex geometries. The accuracy and convergence of the consistent I 2SPH are examined via comparison with analytical solutions, grid-based numerical solutions, or empirical models. Lastly, the new method provides a framework to explore broader applications of SPH in microfluidics and complex fluids with charged objects, such as colloids and biomolecules, in arbitrary complex geometries.

Gas stripping in galaxy clusters: a new SPH simulation approach

NASA Astrophysics Data System (ADS)

Jáchym, P.; Palouš, J.; Köppen, J.; Combes, F.

2007-09-01

Aims:The influence of a time-varying ram pressure on spiral galaxies in clusters is explored with a new simulation method based on the N-body SPH/tree code GADGET. Methods: We have adapted the code to describe the interaction of two different gas phases, the diffuse hot intracluster medium (ICM) and the denser and colder interstellar medium (ISM). Both the ICM and ISM components are introduced as SPH particles. As a galaxy arrives on a highly radial orbit from outskirts to cluster center, it crosses the ICM density peak and experiences a time-varying wind. Results: Depending on the duration and intensity of the ISM-ICM interaction, early and late type galaxies in galaxy clusters with either a large or small ICM distribution are found to show different stripping efficiencies, amounts of reaccretion of the extra-planar ISM, and final masses. We compare the numerical results with analytical approximations of different complexity and indicate the limits of the Gunn & Gott simple stripping formula. Conclusions: Our investigations emphasize the role of the galactic orbital history to the stripping amount. We discuss the contribution of ram pressure stripping to the origin of the ICM and its metallicity. We propose gas accumulations like tails, filaments, or ripples to be responsible for stripping in regions with low overall ICM occurrence. Appendix A is only available in electronic form at http://www.aanda.org

Hydrodynamical simulations of coupled and uncoupled quintessence models - II. Galaxy clusters

NASA Astrophysics Data System (ADS)

Carlesi, Edoardo; Knebe, Alexander; Lewis, Geraint F.; Yepes, Gustavo

2014-04-01

We study the z = 0 properties of clusters (and large groups) of galaxies within the context of interacting and non-interacting quintessence cosmological models, using a series of adiabatic SPH simulations. Initially, we examine the average properties of groups and clusters, quantifying their differences in ΛCold Dark Matter (ΛCDM), uncoupled Dark Energy (uDE) and coupled Dark Energy (cDE) cosmologies. In particular, we focus upon radial profiles of the gas density, temperature and pressure, and we also investigate how the standard hydrodynamic equilibrium hypothesis holds in quintessence cosmologies. While we are able to confirm previous results about the distribution of baryons, we also find that the main discrepancy (with differences up to 20 per cent) can be seen in cluster pressure profiles. We then switch attention to individual structures, mapping each halo in quintessence cosmology to its ΛCDM counterpart. We are able to identify a series of small correlations between the coupling in the dark sector and halo spin, triaxiality and virialization ratio. When looking at spin and virialization of dark matter haloes, we find a weak (5 per cent) but systematic deviation in fifth force scenarios from ΛCDM.

Collisionless stellar hydrodynamics as an efficient alternative to N-body methods

NASA Astrophysics Data System (ADS)

Mitchell, Nigel L.; Vorobyov, Eduard I.; Hensler, Gerhard

2013-01-01

The dominant constituents of the Universe's matter are believed to be collisionless in nature and thus their modelling in any self-consistent simulation is extremely important. For simulations that deal only with dark matter or stellar systems, the conventional N-body technique is fast, memory efficient and relatively simple to implement. However when extending simulations to include the effects of gas physics, mesh codes are at a distinct disadvantage compared to Smooth Particle Hydrodynamics (SPH) codes. Whereas implementing the N-body approach into SPH codes is fairly trivial, the particle-mesh technique used in mesh codes to couple collisionless stars and dark matter to the gas on the mesh has a series of significant scientific and technical limitations. These include spurious entropy generation resulting from discreteness effects, poor load balancing and increased communication overhead which spoil the excellent scaling in massively parallel grid codes. In this paper we propose the use of the collisionless Boltzmann moment equations as a means to model the collisionless material as a fluid on the mesh, implementing it into the massively parallel FLASH Adaptive Mesh Refinement (AMR) code. This approach which we term `collisionless stellar hydrodynamics' enables us to do away with the particle-mesh approach and since the parallelization scheme is identical to that used for the hydrodynamics, it preserves the excellent scaling of the FLASH code already demonstrated on peta-flop machines. We find that the classic hydrodynamic equations and the Boltzmann moment equations can be reconciled under specific conditions, allowing us to generate analytic solutions for collisionless systems using conventional test problems. We confirm the validity of our approach using a suite of demanding test problems, including the use of a modified Sod shock test. By deriving the relevant eigenvalues and eigenvectors of the Boltzmann moment equations, we are able to use high order

Resolved simulations of a granular-fluid flow through a check dam with a SPH-DCDEM model

NASA Astrophysics Data System (ADS)

Birjukovs Canelas, Ricardo; Domínguez, Jose; Crespo, Alejandro; Gómez-Gesteira, Moncho; Ferreira, Rui M. L.

2017-04-01

Debris flows represent some of the most relevant phenomena in geomorphological events. Due to the potential destructiveness of such flows, they are the target of a vast amount of research. Experimental research in laboratory facilities or in the field is fundamental to characterize the fundamental rheological properties of these flows and to provide insights on its structure. However, characterizing interparticle contacts and the structure of the motion of the granular phase is difficult, even in controlled laboratory conditions, and possible only for simple geometries. This work addresses the need for a numerical simulation tool applicable to granular-fluid mixtures featuring high spatial and temporal resolution, thus capable of resolving the motion of individual particles, including all interparticle contacts and susceptible to complement laboratory research. The DualSPHysics meshless numerical implementation based on Smoothed Particle Hydrodynamics (SPH) is expanded with a Distributed Contact Discrete Element Method (DCDEM) in order to explicitly solve the fluid and the solid phase. The specific objective is to test the SPH-DCDEM approach by comparing its results with experimental data. An experimental set-up for stony debris flows in a slit check dam is reproduced numerically, where solid material is introduced through a hopper assuring a constant solid discharge for the considered time interval. With each sediment particle possibly undergoing several simultaneous contacts, thousands of time-evolving interactions are efficiently treated due to the model's algorithmic structure and the HPC implementation of DualSPHysics. The results, comprising mainly of retention curves, are in good agreement with the measurements, correctly reproducing the changes in efficiency with slit spacing and density. The encouraging results, coupled with the prospect of so far unique insights into the internal dynamics of a debris flow show the potential of high-performance resolved

Simulation of Hydrodynamic Ram Phenomenon Using MSC Dytran

DTIC Science & Technology

2014-09-01

impact is unlikely to have detrimental effects on the exit wall of tank due to its rapid extinction in the fluid. The presence of free surface with lower...unlikely to have detrimental effects on the exit wall of tank due to its rapid extinction in the fluid. The presence of free surface with lower...ALE and SPH simulation of the different phases of HRAM, from [13

Modeling and Simulation of Ceramic Arrays to Improve Ballaistic Performance

DTIC Science & Technology

2013-11-01

2219 , 2000 Tile gap is found to increase the DoP as compared to One Tile tiles The next step will be run simulations on narrower and wider gap sizes...experiments described in reference - ARL-TR- 2219 , 2000 □ Tile gap is found to increase the DoP as compared to One Tile tiles □ The next step will be run...L| Al m ^ s\\cr V^ 1 v^ □ Smoothed-particle hydrodynamics (SPH) used for all parts □ SPH size = 0.40-mm, totaling 278k

Three-Dimensional Smoothed Particle Hydrodynamics Modeling of Preferential Flow Dynamics at Fracture Intersections on a High-Performance Computing Platform

NASA Astrophysics Data System (ADS)

Kordilla, J.; Bresinsky, L. T.

2017-12-01

The physical mechanisms that govern preferential flow dynamics in unsaturated fractured rock formations are complex and not well understood. Fracture intersections may act as an integrator of unsaturated flow, leading to temporal delay, intermittent flow and partitioning dynamics. In this work, a three-dimensional Pairwise-Force Smoothed Particle Hydrodynamics (PF-SPH) model is being applied in order to simulate gravity-driven multiphase flow at synthetic fracture intersections. SPH, as a meshless Lagrangian method, is particularly suitable for modeling deformable interfaces, such as three-phase contact dynamics of droplets, rivulets and free-surface films. The static and dynamic contact angle can be recognized as the most important parameter of gravity-driven free-surface flow. In SPH, surface tension and adhesion naturally emerges from the implemented pairwise fluid-fluid (sff) and solid-fluid (ssf) interaction force. The model was calibrated to a contact angle of 65°, which corresponds to the wetting properties of water on Poly(methyl methacrylate). The accuracy of the SPH simulations were validated against an analytical solution of Poiseuille flow between two parallel plates and against laboratory experiments. Using the SPH model, the complex flow mode transitions from droplet to rivulet flow of an experimental study were reproduced. Additionally, laboratory dimensionless scaling experiments of water droplets were successfully replicated in SPH. Finally, SPH simulations were used to investigate the partitioning dynamics of single droplets into synthetic horizontal fractures with various apertures (Δdf = 0, 0.5, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0 mm) and offsets (Δdoff = -1.5, -1.0, -0.5, 0, 1.0, 2.0, 3.0 mm). Fluid masses were measured in the domains R1, R2 and R3. The perfect conditions of ideally smooth surfaces and the SPH inherent advantage of particle tracking allow the recognition of small scale partitioning mechanisms and its importance for bulk flow

FleCSPH - a parallel and distributed SPH implementation based on the FleCSI framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Junghans, Christoph; Loiseau, Julien

2017-06-20

FleCSPH is a multi-physics compact application that exercises FleCSI parallel data structures for tree-based particle methods. In particular, FleCSPH implements a smoothed-particle hydrodynamics (SPH) solver for the solution of Lagrangian problems in astrophysics and cosmology. FleCSPH includes support for gravitational forces using the fast multipole method (FMM).

Constraints on Decreases in Eta Carinae's Mass-loss from 3D Hydrodynamic Simulations of Its Binary Colliding Winds

NASA Technical Reports Server (NTRS)

Madura, T. I.; Gull, T. R.; Okazaki, A. T.; Russell, C. M. P.; Owocki, S. P.; Groh, J. H.; Corcoran, M. F.; Hamaguchi, K.; Teodoro, M.

2013-01-01

Recent work suggests that the mass-loss rate of the primary star Eta-A in the massive colliding wind binary Eta Carinae dropped by a factor of 2-3 between 1999 and 2010. We present result from large- (+/- 1545 au) and small- (+/- 155 au) domain, 3D smoothed particle hydrodynamics (SPH) simulations of Eta Car's colliding winds for three Eta-A mass-loss rates ( (dot-M(sub Eta-A) = 2.4, 4.8 and 8.5 × 10(exp -4) M(solar)/ yr), investigating the effects on the dynamics of the binary wind-wind collision (WWC). These simulations include orbital motion, optically thin radiative cooling and radiative forces. We find that dot-M Eta-A greatly affects the time-dependent hydrodynamics at all spatial scales investigated. The simulations also show that the post-shock wind of the companion star Eta-B switches from the adiabatic to the radiative-cooling regime during periastron passage (Phi approx.= 0.985-1.02). This switchover starts later and ends earlier the lower the value of dot-M Eta-A and is caused by the encroachment of the wind of Eta-A into the acceleration zone of Eta-B's wind, plus radiative inhibition of Eta-B's wind by Eta-A. The SPH simulations together with 1D radiative transfer models of Eta-A's spectra reveal that a factor of 2 or more drop in dot-M EtaA should lead to substantial changes in numerous multiwavelength observables. Recent observations are not fully consistent with the model predictions, indicating that any drop in dot- M Eta-A was likely by a factor of approx. < 2 and occurred after 2004. We speculate that most of the recent observed changes in Eta Car are due to a small increase in the WWC opening angle that produces significant effects because our line of sight to the system lies close to the dense walls of the WWC zone. A modest decrease in dot-M Eta-A may be responsible, but changes in the wind/stellar parameter of Eta-B, while less likely, cannot yet be fully ruled out. We suggest observations during Eta-Car's next periastron in 2014 to further

Effect of Unsaturated Flow Modes on Partitioning Dynamics of Gravity-Driven Flow at a Simple Fracture Intersection: Laboratory Study and Three-Dimensional Smoothed Particle Hydrodynamics Simulations

NASA Astrophysics Data System (ADS)

Kordilla, Jannes; Noffz, Torsten; Dentz, Marco; Geyer, Tobias; Tartakovsky, Alexandre M.

2017-11-01

In this work, we study gravity-driven flow of water in the presence of air on a synthetic surface intersected by a horizontal fracture and investigate the importance of droplet and rivulet flow modes on the partitioning behavior at the fracture intersection. We present laboratory experiments, three-dimensional smoothed particle hydrodynamics (SPH) simulations using a heavily parallelized code, and a theoretical analysis. The flow-rate-dependent mode switching from droplets to rivulets is observed in experiments and reproduced by the SPH model, and the transition ranges agree in SPH simulations and laboratory experiments. We show that flow modes heavily influence the "bypass" behavior of water flowing along a fracture junction. Flows favoring the formation of droplets exhibit a much stronger bypass capacity compared to rivulet flows, where nearly the whole fluid mass is initially stored within the horizontal fracture. The effect of fluid buffering within the horizontal fracture is presented in terms of dimensionless fracture inflow so that characteristic scaling regimes can be recovered. For both cases (rivulets and droplets), the flow within the horizontal fracture transitions into a Washburn regime until a critical threshold is reached and the bypass efficiency increases. For rivulet flows, the initial filling of the horizontal fracture is described by classical plug flow. Meanwhile, for droplet flows, a size-dependent partitioning behavior is observed, and the filling of the fracture takes longer. For the case of rivulet flow, we provide an analytical solution that demonstrates the existence of classical Washburn flow within the horizontal fracture.

MODA: a new algorithm to compute optical depths in multidimensional hydrodynamic simulations

NASA Astrophysics Data System (ADS)

Perego, Albino; Gafton, Emanuel; Cabezón, Rubén; Rosswog, Stephan; Liebendörfer, Matthias

2014-08-01

Aims: We introduce the multidimensional optical depth algorithm (MODA) for the calculation of optical depths in approximate multidimensional radiative transport schemes, equally applicable to neutrinos and photons. Motivated by (but not limited to) neutrino transport in three-dimensional simulations of core-collapse supernovae and neutron star mergers, our method makes no assumptions about the geometry of the matter distribution, apart from expecting optically transparent boundaries. Methods: Based on local information about opacities, the algorithm figures out an escape route that tends to minimize the optical depth without assuming any predefined paths for radiation. Its adaptivity makes it suitable for a variety of astrophysical settings with complicated geometry (e.g., core-collapse supernovae, compact binary mergers, tidal disruptions, star formation, etc.). We implement the MODA algorithm into both a Eulerian hydrodynamics code with a fixed, uniform grid and into an SPH code where we use a tree structure that is otherwise used for searching neighbors and calculating gravity. Results: In a series of numerical experiments, we compare the MODA results with analytically known solutions. We also use snapshots from actual 3D simulations and compare the results of MODA with those obtained with other methods, such as the global and local ray-by-ray method. It turns out that MODA achieves excellent accuracy at a moderate computational cost. In appendix we also discuss implementation details and parallelization strategies.

The moving-least-squares-particle hydrodynamics method (MLSPH)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dilts, G.

1997-12-31

An enhancement of the smooth-particle hydrodynamics (SPH) method has been developed using the moving-least-squares (MLS) interpolants of Lancaster and Salkauskas which simultaneously relieves the method of several well-known undesirable behaviors, including spurious boundary effects, inaccurate strain and rotation rates, pressure spikes at impact boundaries, and the infamous tension instability. The classical SPH method is derived in a novel manner by means of a Galerkin approximation applied to the Lagrangian equations of motion for continua using as basis functions the SPH kernel function multiplied by the particle volume. This derivation is then modified by simply substituting the MLS interpolants for themore » SPH Galerkin basis, taking care to redefine the particle volume and mass appropriately. The familiar SPH kernel approximation is now equivalent to a colocation-Galerkin method. Both classical conservative and recent non-conservative formulations of SPH can be derived and emulated. The non-conservative forms can be made conservative by adding terms that are zero within the approximation at the expense of boundary-value considerations. The familiar Monaghan viscosity is used. Test calculations of uniformly expanding fluids, the Swegle example, spinning solid disks, impacting bars, and spherically symmetric flow illustrate the superiority of the technique over SPH. In all cases it is seen that the marvelous ability of the MLS interpolants to add up correctly everywhere civilizes the noisy, unpredictable nature of SPH. Being a relatively minor perturbation of the SPH method, it is easily retrofitted into existing SPH codes. On the down side, computational expense at this point is significant, the Monaghan viscosity undoes the contribution of the MLS interpolants, and one-point quadrature (colocation) is not accurate enough. Solutions to these difficulties are being pursued vigorously.« less

A smoothed particle hydrodynamics model for electrostatic transport of charged lunar dust on the moon surface

NASA Astrophysics Data System (ADS)

Mao, Zirui; Liu, G. R.

2018-02-01

The behavior of lunar dust on the Moon surface is quite complicated compared to that on the Earth surface due to the small lunar gravity and the significant influence of the complicated electrostatic filed in the Universe. Understanding such behavior is critical for the exploration of the Moon. This work develops a smoothed particle hydrodynamics (SPH) model with the elastic-perfectly plastic constitutive equation and Drucker-Prager yield criterion to simulate the electrostatic transporting of multiple charged lunar dust particles. The initial electric field is generated based on the particle-in-cell method and then is superposed with the additional electric field from the charged dust particles to obtain the resultant electric field in the following process. Simulations of cohesive soil's natural failure and electrostatic transport of charged soil under the given electric force and gravity were carried out using the SPH model. Results obtained in this paper show that the negatively charged dust particles levitate and transport to the shadow area with a higher potential from the light area with a lower potential. The motion of soil particles finally comes to a stable state. The numerical result for final distribution of soil particles and potential profile above planar surface by the SPH method matches well with the experimental result, and the SPH solution looks sound in the maximum levitation height prediction of lunar dust under an uniform electric field compared to theoretical solution, which prove that SPH is a reliable method in describing the behavior of soil particles under a complicated electric field and small gravity field with the consideration of interactions among soil particles.

Protein modeling and molecular dynamics simulation of the two novel surfactant proteins SP-G and SP-H.

PubMed

Rausch, Felix; Schicht, Martin; Bräuer, Lars; Paulsen, Friedrich; Brandt, Wolfgang

2014-11-01

Surfactant proteins are well known from the human lung where they are responsible for the stability and flexibility of the pulmonary surfactant system. They are able to influence the surface tension of the gas-liquid interface specifically by directly interacting with single lipids. This work describes the generation of reliable protein structure models to support the experimental characterization of two novel putative surfactant proteins called SP-G and SP-H. The obtained protein models were complemented by predicted posttranslational modifications and placed in a lipid model system mimicking the pulmonary surface. Molecular dynamics simulations of these protein-lipid systems showed the stability of the protein models and the formation of interactions between protein surface and lipid head groups on an atomic scale. Thereby, interaction interface and strength seem to be dependent on orientation and posttranslational modification of the protein. The here presented modeling was fundamental for experimental localization studies and the simulations showed that SP-G and SP-H are theoretically able to interact with lipid systems and thus are members of the surfactant protein family.

A CSF-SPH method for simulating drainage and imbibition at pore-scale resolution while tracking interfacial areas

NASA Astrophysics Data System (ADS)

Sivanesapillai, Rakulan; Falkner, Nadine; Hartmaier, Alexander; Steeb, Holger

2016-09-01

We present a conservative smoothed particle hydrodynamics (SPH) model to study the flow of multiple, immiscible fluid phases in porous media using direct pore-scale simulations. Particular focus is put on continuously tracking the evolution of interfacial areas, which are considered to be important morphological quantities affecting multiphase transport in porous media. In addition to solving the Navier-Stokes equations, the model accounts for the effects of capillarity at interfaces and contact lines. This is done by means of incorporating the governing interfacial mass and momentum balances using the continuum surface force (CSF) method, thus rendering model calibration routines unnecessary and minimizing the set of constitutive and kinematic assumptions. We address the application of boundary conditions at rigid solid surfaces and study the predictive capability of the model as well as optimal choices for numerical parameters using an extensive model validation procedure. We demonstrate the applicability of the model to simulate multiphase flows involving partial wettability, dynamic effects, large density ratios (up to 1000), large viscosity ratios (up to 100), as well as fragmentation and coalescence of fluid phases. The model is used to study the evolution of fluid-fluid interfacial areas during saturation-controlled primary drainage and main imbibition of heterogeneous pore spaces at low capillary numbers. A variety of pore-scale effects, such as wetting phase entrapment and fragmentation due to snap-off, are observed. Specific fluid-fluid interfacial area is observed to monotonically increase during primary drainage and hysteretic effects are apparent during main imbibition.

Smooth Particle Hydrodynamics-based Wind Representation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prescott, Steven; Smith, Curtis; Hess, Stephen

2016-12-01

As a result of the 2011 accident at the Fukushima Dai-ichi NPP and other operational NPP experience, there is an identified need to better characterize and evaluate the potential impacts of externally generated hazards on NPP safety. Due to the ubiquitous occurrence of high winds around the world and the possible extreme magnitude of the hazard that has been observed, the assessment of the impact of the high-winds hazard has been identified as an important activity by both NPP owner-operators and regulatory authorities. However, recent experience obtained from the conduct of high-winds risk assessments indicates that such activities have beenmore » both labor-intensive and expensive to perform. Additionally, the existing suite of methods and tools to conduct such assessments (which were developed decades ago) do not make use of modern computational architectures (e.g., parallel processing, object-oriented programming techniques, or simple user interfaces) or methods (e.g., efficient and robust numerical-solution schemes). As a result, the current suite of methods and tools will rapidly become obsolete. Physics-based 3D simulation methods can provide information to assist in the RISMC PRA methodology. This research is intended to determine what benefits SPH methods could bring to high-winds simulations for the purposes of assessing their potential impact on NPP safety. The initial investigation has determined that SPH can simulate key areas of high-wind events with reasonable accuracy, compared to other methods. Some problems, such as simulation voids, need to be addressed, but possible solutions have been identified and will be tested with continued work. This work also demonstrated that SPH simulations can provide a means for simulating debris movement; however, further investigations into the capability to determine the impact of high winds and the impacts of wind-driven debris that lead to SSC failures need to be done. SPH simulations alone would be limited in

Murine recessive hereditary spherocytosis, sph/sph, is caused by a mutation in the erythroid alpha-spectrin gene.

PubMed

Wandersee, N J; Birkenmeier, C S; Gifford, E J; Mohandas, N; Barker, J E

2000-01-01

Spectrin, a heterodimer of alpha- and beta-subunits, is the major protein component of the red blood cell membrane skeleton. The mouse mutation, sph, causes an alpha-spectrin-deficient hereditary spherocytosis with the severe phenotype typical of recessive hereditary spherocytosis in humans. The sph mutation maps to the erythroid alpha-spectrin locus, Spna1, on Chromosome 1. Scanning electron microscopy, osmotic gradient ektacytometry, cDNA cloning, RT-PCR, nucleic acid sequencing, and Northern blot analyses were used to characterize the wild type and sph alleles of the Spna1 locus. Our results confirm the spherocytic nature of sph/sph red blood cells and document a mild spherocytic transition in the +/sph heterozygotes. Sequencing of the full length coding region of the Spna1 wild type allele from the C57BL/6J strain of mice reveals a 2414 residue deduced amino acid sequence that shows the typical 106-amino-acid repeat structure previously described for other members of the spectrin protein family. Sequence analysis of RT-PCR clones from sph/sph alpha-spectrin mRNA identified a single base deletion in repeat 5 that would cause a frame shift and premature termination of the protein. This deletion was confirmed in sph/sph genomic DNA. Northern blot analyses of the distribution of Spna1 mRNA in non-erythroid tissues detects the expression of 8, 2.5 and 2.0 kb transcripts in adult heart. These results predict the heart as an additional site where alpha-spectrin mutations may produce a phenotype and raise the possibility that a novel functional class of small alpha-spectrin isoforms may exist.

Multi-phase SPH model for simulation of erosion and scouring by means of the shields and Drucker-Prager criteria.

NASA Astrophysics Data System (ADS)

Zubeldia, Elizabeth H.; Fourtakas, Georgios; Rogers, Benedict D.; Farias, Márcio M.

2018-07-01

A two-phase numerical model using Smoothed Particle Hydrodynamics (SPH) is developed to model the scouring of two-phase liquid-sediments flows with large deformation. The rheology of sediment scouring due to flows with slow kinematics and high shear forces presents a challenge in terms of spurious numerical fluctuations. This paper bridges the gap between the non-Newtonian and Newtonian flows by proposing a model that combines the yielding, shear and suspension layer mechanics which are needed to predict accurately the local erosion phenomena. A critical bed-mobility condition based on the Shields criterion is imposed to the particles located at the sediment surface. Thus, the onset of the erosion process is independent on the pressure field and eliminates the numerical problem of pressure dependant erosion at the interface. This is combined with the Drucker-Prager yield criterion to predict the onset of yielding of the sediment surface and a concentration suspension model. The multi-phase model has been implemented in the open-source DualSPHysics code accelerated with a graphics processing unit (GPU). The multi-phase model has been compared with 2-D reference numerical models and new experimental data for scour with convergent results. Numerical results for a dry-bed dam break over an erodible bed shows improved agreement with experimental scour and water surface profiles compared to well-known SPH multi-phase models.

Three-Dimensional Hydrodynamic Simulations of OMEGA Implosions

NASA Astrophysics Data System (ADS)

Igumenshchev, I. V.

2016-10-01

The effects of large-scale (with Legendre modes less than 30) asymmetries in OMEGA direct-drive implosions caused by laser illumination nonuniformities (beam-power imbalance and beam mispointing and mistiming) and target offset, mount, and layers nonuniformities were investigated using three-dimensional (3-D) hydrodynamic simulations. Simulations indicate that the performance degradation in cryogenic implosions is caused mainly by the target offsets ( 10 to 20 μm), beampower imbalance (σrms 10 %), and initial target asymmetry ( 5% ρRvariation), which distort implosion cores, resulting in a reduced hot-spot confinement and an increased residual kinetic energy of the stagnated target. The ion temperature inferred from the width of simulated neutron spectra are influenced by bulk fuel motion in the distorted hot spot and can result in up to 2-keV apparent temperature increase. Similar temperature variations along different lines of sight are observed. Simulated x-ray images of implosion cores in the 4- to 8-keV energy range show good agreement with experiments. Demonstrating hydrodynamic equivalence to ignition designs on OMEGA requires reducing large-scale target and laser-imposed nonuniformities, minimizing target offset, and employing high-efficient mid-adiabat (α = 4) implosion designs that mitigate cross-beam energy transfer (CBET) and suppress short-wavelength Rayleigh-Taylor growth. These simulations use a new low-noise 3-D Eulerian hydrodynamic code ASTER. Existing 3-D hydrodynamic codes for direct-drive implosions currently miss CBET and noise-free ray-trace laser deposition algorithms. ASTER overcomes these limitations using a simplified 3-D laser-deposition model, which includes CBET and is capable of simulating the effects of beam-power imbalance, beam mispointing, mistiming, and target offset. This material is based upon work supported by the Department of Energy National Nuclear Security Administration under Award Number DE-NA0001944.

A hybrid Lagrangian Voronoi-SPH scheme

NASA Astrophysics Data System (ADS)

Fernandez-Gutierrez, D.; Souto-Iglesias, A.; Zohdi, T. I.

2018-07-01

A hybrid Lagrangian Voronoi-SPH scheme, with an explicit weakly compressible formulation for both the Voronoi and SPH sub-domains, has been developed. The SPH discretization is substituted by Voronoi elements close to solid boundaries, where SPH consistency and boundary conditions implementation become problematic. A buffer zone to couple the dynamics of both sub-domains is used. This zone is formed by a set of particles where fields are interpolated taking into account SPH particles and Voronoi elements. A particle may move in or out of the buffer zone depending on its proximity to a solid boundary. The accuracy of the coupled scheme is discussed by means of a set of well-known verification benchmarks.

A hybrid Lagrangian Voronoi-SPH scheme

NASA Astrophysics Data System (ADS)

Fernandez-Gutierrez, D.; Souto-Iglesias, A.; Zohdi, T. I.

2017-11-01

A hybrid Lagrangian Voronoi-SPH scheme, with an explicit weakly compressible formulation for both the Voronoi and SPH sub-domains, has been developed. The SPH discretization is substituted by Voronoi elements close to solid boundaries, where SPH consistency and boundary conditions implementation become problematic. A buffer zone to couple the dynamics of both sub-domains is used. This zone is formed by a set of particles where fields are interpolated taking into account SPH particles and Voronoi elements. A particle may move in or out of the buffer zone depending on its proximity to a solid boundary. The accuracy of the coupled scheme is discussed by means of a set of well-known verification benchmarks.

SEURAT: SPH scheme extended with ultraviolet line radiative transfer

NASA Astrophysics Data System (ADS)

Abe, Makito; Suzuki, Hiroyuki; Hasegawa, Kenji; Semelin, Benoit; Yajima, Hidenobu; Umemura, Masayuki

2018-05-01

We present a novel Lyman alpha (Ly α) radiative transfer code, SEURAT (SPH scheme Extended with Ultraviolet line RAdiative Transfer), where line scatterings are solved adaptively with the resolution of the smoothed particle hydrodynamics (SPH). The radiative transfer method implemented in SEURAT is based on a Monte Carlo algorithm in which the scattering and absorption by dust are also incorporated. We perform standard test calculations to verify the validity of the code; (i) emergent spectra from a static uniform sphere, (ii) emergent spectra from an expanding uniform sphere, and (iii) escape fraction from a dusty slab. Thereby, we demonstrate that our code solves the {Ly} α radiative transfer with sufficient accuracy. We emphasize that SEURAT can treat the transfer of {Ly} α photons even in highly complex systems that have significantly inhomogeneous density fields. The high adaptivity of SEURAT is desirable to solve the propagation of {Ly} α photons in the interstellar medium of young star-forming galaxies like {Ly} α emitters (LAEs). Thus, SEURAT provides a powerful tool to model the emergent spectra of {Ly} α emission, which can be compared to the observations of LAEs.

SPH investigation of the thermal effects on the fluid mixing in a microchannel with rotating stirrers

NASA Astrophysics Data System (ADS)

Shamsoddini, Rahim

2018-04-01

An incompressible smoothed particle hydrodynamics algorithm is proposed to model and investigate the thermal effect on the mixing rate of an active micromixer in which the rotating stirrers enhance the mixing rate. In liquids, mass diffusion increases with increasing temperature, while viscosity decreases; so, the local Schmidt number decreases considerably with increasing temperature. The present study investigates the effect of wall temperature on mixing rate with an improved SPH method. The robust SPH method used in the present work is equipped with a shifting algorithm and renormalization tensors. By introducing this new algorithm, the several mass, momentum, energy, and concentration equations are solved. The results, discussed for different temperature ratios, show that mixing rate increases significantly with increased temperature ratio.

A novel SPH method for sedimentation in a turbulent fluid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kwon, Jihoe; Monaghan, J.J., E-mail: joe.monaghan@sci.monash.edu.au

2015-11-01

A novel method for simulating sedimentation is described and applied to the sedimentation of dust in a turbulent fluid. We assume the dust grains are sufficiently numerous that they may be treated as a fluid and modelled by SPH particles. A different set of SPH particles describes the fluid. The equations of motion are therefore similar to those of Monaghan and Kocharyan [14] with the exception that the sedimentation of dust onto a solid surface is treated as if the surface mimics a sink for the dust fluid. The continuity equation for the dust then contains a sink term thatmore » can be modelled in the SPH formulation by allowing the mass of each SPH dust particle to decrease when it is sufficiently close to the boundary. We apply this method both to sedimentation in a nearly static fluid, and to sedimentation in a turbulent fluid. In the latter case we produce the turbulence by both a mechanical stirrer and by a stochastic algorithm. Our results agree very closely with the experiments of Martin and Nokes.« less

Modeling and Simulation of Ceramic Arrays to Improve Ballistic Performance

DTIC Science & Technology

2014-04-30

experiments (tiles from Supplier, sintered SiC) 15. SUBJECT TERMS Adhesive Layer Effect, .30cal AP M2 Projectile, 762x39 PS Projectile, SPH , Aluminum...Aluminum (AI5083) □ Impacts by .30cal AP-M2 projectile and are modeled using SPH elements in AutoDyn □ Center strike model validation runs with SiC tiles...View SiC\\ Front View □ Smoothed-particle hydrodynamics ( SPH ) used for al parts J SPH Size 0.4 used initially □ SPH Size 0.2 used to capture

Investigating mixing and emptying for aqueous liquid content from the stomach using a coupled biomechanical-SPH model.

PubMed

Harrison, Simon M; Cleary, Paul W; Sinnott, Matthew D

2018-05-18

The stomach is a critical organ for food digestion but it is not well understood how it operates, either when healthy or when dysfunction occurs. Stomach function depends on the timing and amplitude of wall contractions, the fill level and the type of gastric content. Using a coupled biomechanical-Smoothed Particle Hydrodynamics (B-SPH) model, we investigate how gastric discharge is affected by the contraction behaviour of the stomach wall and the viscosity of the content. The results of the model provide new insights into how the content viscosity and the number of compression waves down the length of the stomach affect the mixing within and the discharge rate of the content exiting from the stomach to the duodenum. This investigation shows that the B-SPH model is capable of simulating complicated stomach behaviour. The rate of gastric emptying is found to increase with a smaller period in between contractile waves and to have a nonlinear relationship with content viscosity. Increased resistance to flow into the duodenum is also shown to reduce the rate of emptying. The degree of gastric mixing is found to be insensitive to changes in the period between contractile waves for fluid with a viscosity of water but to be substantially affected by the viscosity of the gastric content.

Efficient high-quality volume rendering of SPH data.

PubMed

Fraedrich, Roland; Auer, Stefan; Westermann, Rüdiger

2010-01-01

High quality volume rendering of SPH data requires a complex order-dependent resampling of particle quantities along the view rays. In this paper we present an efficient approach to perform this task using a novel view-space discretization of the simulation domain. Our method draws upon recent work on GPU-based particle voxelization for the efficient resampling of particles into uniform grids. We propose a new technique that leverages a perspective grid to adaptively discretize the view-volume, giving rise to a continuous level-of-detail sampling structure and reducing memory requirements compared to a uniform grid. In combination with a level-of-detail representation of the particle set, the perspective grid allows effectively reducing the amount of primitives to be processed at run-time. We demonstrate the quality and performance of our method for the rendering of fluid and gas dynamics SPH simulations consisting of many millions of particles.

A 3D smoothed particle hydrodynamics model for erosional dam-break floods

NASA Astrophysics Data System (ADS)

Amicarelli, Andrea; Kocak, Bozhana; Sibilla, Stefano; Grabe, Jürgen

2017-11-01

A mesh-less smoothed particle hydrodynamics (SPH) model for bed-load transport on erosional dam-break floods is presented. This mixture model describes both the liquid phase and the solid granular material. The model is validated on the results from several experiments on erosional dam breaks. A comparison between the present model and a 2-phase SPH model for geotechnical applications (Gadget Soil; TUHH) is performed. A demonstrative 3D erosional dam break on complex topography is investigated. The present 3D mixture model is characterised by: no tuning parameter for the mixture viscosity; consistency with the Kinetic Theory of Granular Flow; ability to reproduce the evolution of the free surface and the bed-load transport layer; applicability to practical problems in civil engineering. The numerical developments of this study are represented by a new SPH scheme for bed-load transport, which is implemented in the SPH code SPHERA v.8.0 (RSE SpA), distributed as FOSS on GitHub.

Comparing Results of SPH/N-body Impact Simulations Using Both Solid and Rubble-pile Target Asteroids

NASA Astrophysics Data System (ADS)

Durda, Daniel D.; Bottke, W. F.; Enke, B. L.; Nesvorný, D.; Asphaug, E.; Richardson, D. C.

2006-09-01

We have been investigating the properties of satellites and the morphology of size-frequency distributions (SFDs) resulting from a suite of 160 SPH/N-body simulations of impacts into 100-km diameter parent asteroids (Durda et al. 2004, Icarus 170, 243-257; Durda et al. 2006, Icarus, in press). These simulations have produced many valuable insights into the outcomes of cratering and disruptive impacts but were limited to monolithic basalt targets. As a natural consequence of collisional evolution, however, many asteroids have undergone a series of battering impacts that likely have left their interiors substantially fractured, if not completely rubblized. In light of this, we have re-mapped the matrix of simulations using rubble-pile target objects. We constructed the rubble-pile targets by filling the interior of the 100-km diameter spherical shell (the target envelope) with randomly sized solid spheres in mutual contact. We then assigned full damage (which reduces tensile and shear stresses to zero) to SPH particles in the contacts between the components; the remaining volume is void space. The internal spherical components have a power-law distribution of sizes simulating fragments of a pre-shattered parent object. First-look analysis of the rubble-pile results indicate some general similarities to the simulations with the monolithic targets (e.g., similar trends in the number of small, gravitationally bound satellite systems as a function of impact conditions) and some significant differences (e.g., size of largest remnants and smaller debris affecting size frequency distributions of resulting families). We will report details of a more thorough analysis and the implications for collisional models of the main asteroid belt. This work is supported by the National Science Foundation, grant number AST0407045.

Multi-resolution Delta-plus-SPH with tensile instability control: Towards high Reynolds number flows

NASA Astrophysics Data System (ADS)

Sun, P. N.; Colagrossi, A.; Marrone, S.; Antuono, M.; Zhang, A. M.

2018-03-01

It is well known that the use of SPH models in simulating flow at high Reynolds numbers is limited because of the tensile instability inception in the fluid region characterized by high vorticity and negative pressure. In order to overcome this issue, the δ+-SPH scheme is modified by implementing a Tensile Instability Control (TIC). The latter consists of switching the momentum equation to a non-conservative formulation in the unstable flow regions. The loss of conservation properties is shown to induce small errors, provided that the particle distribution is regular. The latter condition can be ensured thanks to the implementation of a Particle Shifting Technique (PST). The novel variant of the δ+-SPH is proved to be effective in preventing the onset of tensile instability. Several challenging benchmark tests involving flows past bodies at large Reynolds numbers have been used. Within this a simulation characterized by a deforming foil that resembles a fish-like swimming body is used as a practical application of the δ+-SPH model in biological fluid mechanics.

An arbitrary boundary with ghost particles incorporated in coupled FEM-SPH model for FSI problems

NASA Astrophysics Data System (ADS)

Long, Ting; Hu, Dean; Wan, Detao; Zhuang, Chen; Yang, Gang

2017-12-01

It is important to treat the arbitrary boundary of Fluid-Structure Interaction (FSI) problems in computational mechanics. In order to ensure complete support condition and restore the first-order consistency near the boundary of Smoothed Particle Hydrodynamics (SPH) method for coupling Finite Element Method (FEM) with SPH model, a new ghost particle method is proposed by dividing the interceptive area of kernel support domain into subareas corresponding to boundary segments of structure. The ghost particles are produced automatically for every fluid particle at each time step, and the properties of ghost particles, such as density, mass and velocity, are defined by using the subareas to satisfy the boundary condition. In the coupled FEM-SPH model, the normal and shear forces from a boundary segment of structure to a fluid particle are calculated through the corresponding ghost particles, and its opposite forces are exerted on the corresponding boundary segment, then the momentum of the present method is conservation and there is no matching requirements between the size of elements and the size of particles. The performance of the present method is discussed and validated by several FSI problems with complex geometry boundary and moving boundary.

SPH modeling of fluid-solid interaction for dynamic failure analysis of fluid-filled thin shells

NASA Astrophysics Data System (ADS)

Caleyron, F.; Combescure, A.; Faucher, V.; Potapov, S.

2013-05-01

This work concerns the prediction of failure of a fluid-filled tank under impact loading, including the resulting fluid leakage. A water-filled steel cylinder associated with a piston is impacted by a mass falling at a prescribed velocity. The cylinder is closed at its base by an aluminum plate whose characteristics are allowed to vary. The impact on the piston creates a pressure wave in the fluid which is responsible for the deformation of the plate and, possibly, the propagation of cracks. The structural part of the problem is modeled using Mindlin-Reissner finite elements (FE) and Smoothed Particle Hydrodynamics (SPH) shells. The modeling of the fluid is also based on an SPH formulation. The problem involves significant fluid-structure interactions (FSI) which are handled through a master-slave-based method and the pinballs method. Numerical results are compared to experimental data.

Simulating coupled dynamics of a rigid-flexible multibody system and compressible fluid

NASA Astrophysics Data System (ADS)

Hu, Wei; Tian, Qiang; Hu, HaiYan

2018-04-01

As a subsequent work of previous studies of authors, a new parallel computation approach is proposed to simulate the coupled dynamics of a rigid-flexible multibody system and compressible fluid. In this approach, the smoothed particle hydrodynamics (SPH) method is used to model the compressible fluid, the natural coordinate formulation (NCF) and absolute nodal coordinate formulation (ANCF) are used to model the rigid and flexible bodies, respectively. In order to model the compressible fluid properly and efficiently via SPH method, three measures are taken as follows. The first is to use the Riemann solver to cope with the fluid compressibility, the second is to define virtual particles of SPH to model the dynamic interaction between the fluid and the multibody system, and the third is to impose the boundary conditions of periodical inflow and outflow to reduce the number of SPH particles involved in the computation process. Afterwards, a parallel computation strategy is proposed based on the graphics processing unit (GPU) to detect the neighboring SPH particles and to solve the dynamic equations of SPH particles in order to improve the computation efficiency. Meanwhile, the generalized-alpha algorithm is used to solve the dynamic equations of the multibody system. Finally, four case studies are given to validate the proposed parallel computation approach.

Modeling and Simulation of Ceramic Arrays to Improve Ballistic Performance

DTIC Science & Technology

2014-03-01

30cal AP M2 Projectile, 762x39 PS Projectile, SPH , Aluminum 5083, SiC, DoP Expeminets, AutoDyn Sin 16. SECURITY CLASSIFICATION OF: UU a. REPORT b...projectile and are modeled using SPH elements in AutoDyn □ Center strike model validation runs with SiC tiles are conducted based on the DOP...Smoothed-particle hydrodynamics ( SPH ) used for all parts, SPH Size = 0.2 3 SiC and SiC 2 are identical in properties and dimensions

Variational principles for relativistic smoothed particle hydrodynamics

NASA Astrophysics Data System (ADS)

Monaghan, J. J.; Price, D. J.

2001-12-01

In this paper we show how the equations of motion for the smoothed particle hydrodynamics (SPH) method may be derived from a variational principle for both non-relativistic and relativistic motion when there is no dissipation. Because the SPH density is a function of the coordinates the derivation of the equations of motion through variational principles is simpler than in the continuum case where the density is defined through the continuity equation. In particular, the derivation of the general relativistic equations is more direct and simpler than that of Fock. The symmetry properties of the Lagrangian lead immediately to the familiar additive conservation laws of linear and angular momentum and energy. In addition, we show that there is an approximately conserved quantity which, in the continuum limit, is the circulation.

The growth of central and satellite galaxies in cosmological smoothed particle hydrodynamics simulations

NASA Astrophysics Data System (ADS)

Simha, Vimal; Weinberg, David H.; Davé, Romeel; Gnedin, Oleg Y.; Katz, Neal; Kereš, Dušan

2009-10-01

We examine the accretion and merger histories of central and satellite galaxies in a smoothed particle hydrodynamics (SPH) cosmological simulation that resolves galaxies down to 7 × 109Msolar. Most friends-of-friends haloes in the simulation have a distinct central galaxy, typically 2-5 times more massive than the most massive satellite. As expected, satellites have systematically higher assembly redshifts than central galaxies of the same baryonic mass, and satellites in more massive haloes form earlier. However, contrary to the simplest expectations, satellite galaxies continue to accrete gas and convert it to stars; the gas accretion declines steadily over a period of 0.5-1 Gyr after the satellite halo merges with a larger parent halo. Satellites in a cluster mass halo eventually begin to lose baryonic mass. Typically, satellites in our simulation are 0.1-0.2 mag bluer than in models that assume no gas accretion on to satellites after a halo merger. Since z = 1, 27 per cent of central galaxies (above 3 × 1010Msolar) and 22 per cent of present-day satellite galaxies have merged with a smaller system above a 1:4 mass ratio; about half of the satellite mergers occurred after the galaxy became a satellite and half before. In effect, satellite galaxies can remain `central' objects of halo substructures, with continuing accretion and mergers, making the transition in assembly histories and physical properties a gradual one. Implementing such a gradual transformation in semi-analytic models would improve their agreement with observed colour distributions of satellite galaxies in groups and with the observed colour dependence of galaxy clustering.

Integration of UAV photogrammetry and SPH modelling of fluids to study runoff on real terrains.

PubMed

Barreiro, Anxo; Domínguez, Jose M; C Crespo, Alejandro J; González-Jorge, Higinio; Roca, David; Gómez-Gesteira, Moncho

2014-01-01

Roads can experience runoff problems due to the intense rain discharge associated to severe storms. Two advanced tools are combined to analyse the interaction of complex water flows with real terrains. UAV (Unmanned Aerial Vehicle) photogrammetry is employed to obtain accurate topographic information on small areas, typically on the order of a few hectares. The Smoothed Particle Hydrodynamics (SPH) technique is applied by means of the DualSPHysics model to compute the trajectory of the water flow during extreme rain events. The use of engineering solutions to palliate flood events is also analysed. The study case simulates how the collected water can flow into a close road and how precautionary measures can be effective to drain water under extreme conditions. The amount of water arriving at the road is calculated under different protection scenarios and the efficiency of a ditch is observed to decrease when sedimentation reduces its depth.

Integration of UAV Photogrammetry and SPH Modelling of Fluids to Study Runoff on Real Terrains

PubMed Central

Barreiro, Anxo; Domínguez, Jose M.; C. Crespo, Alejandro J.; González-Jorge, Higinio; Roca, David; Gómez-Gesteira, Moncho

2014-01-01

Roads can experience runoff problems due to the intense rain discharge associated to severe storms. Two advanced tools are combined to analyse the interaction of complex water flows with real terrains. UAV (Unmanned Aerial Vehicle) photogrammetry is employed to obtain accurate topographic information on small areas, typically on the order of a few hectares. The Smoothed Particle Hydrodynamics (SPH) technique is applied by means of the DualSPHysics model to compute the trajectory of the water flow during extreme rain events. The use of engineering solutions to palliate flood events is also analysed. The study case simulates how the collected water can flow into a close road and how precautionary measures can be effective to drain water under extreme conditions. The amount of water arriving at the road is calculated under different protection scenarios and the efficiency of a ditch is observed to decrease when sedimentation reduces its depth. PMID:25372035

A micro-macro coupling approach of MD-SPH method for reactive energetic materials

NASA Astrophysics Data System (ADS)

Liu, Gui Rong; Wang, Guang Yu; Peng, Qing; De, Suvranu

2017-01-01

The simulation of reactive energetic materials has long been the interest of researchers because of the extensive applications of explosives. Much research has been done on the subject at macro scale in the past and research at micro scale has been initiated recently. Equation of state (EoS) is the relation between physical quantities (pressure, temperature, energy and volume) describing thermodynamic states of materials under a given set of conditions. It plays a significant role in determining the characteristics of energetic materials, including Chapman-Jouguet point and detonation velocity. Furthermore, EoS is the key to connect microscopic and macroscopic phenomenon when simulating the macro effects of an explosion. For instance, an ignition and growth model for high explosives uses two JWL EoSs, one for solid explosive and the other for gaseous products, which are often obtained from experiments that can be quite expensive and hazardous. Therefore, it is ideal to calculate the EoS of energetic materials through computational means. In this paper, the EoSs for both solid and gaseous products of β-HMX are calculated using molecular dynamics simulation with ReaxFF-d3, a reactive force field obtained from quantum mechanics. The microscopic simulation results are then compared with experiments and the continuum ignition and growth model. Good agreement is observed. Then, the EoSs obtained through micro-scale simulation is applied in a smoothed particle hydrodynamics (SPH) code to simulate the macro effects of explosions. Simulation results are compared with experiments.

StarSmasher: Smoothed Particle Hydrodynamics code for smashing stars and planets

NASA Astrophysics Data System (ADS)

Gaburov, Evghenii; Lombardi, James C., Jr.; Portegies Zwart, Simon; Rasio, F. A.

2018-05-01

Smoothed Particle Hydrodynamics (SPH) is a Lagrangian particle method that approximates a continuous fluid as discrete nodes, each carrying various parameters such as mass, position, velocity, pressure, and temperature. In an SPH simulation the resolution scales with the particle density; StarSmasher is able to handle both equal-mass and equal number-density particle models. StarSmasher solves for hydro forces by calculating the pressure for each particle as a function of the particle's properties - density, internal energy, and internal properties (e.g. temperature and mean molecular weight). The code implements variational equations of motion and libraries to calculate the gravitational forces between particles using direct summation on NVIDIA graphics cards. Using a direct summation instead of a tree-based algorithm for gravity increases the accuracy of the gravity calculations at the cost of speed. The code uses a cubic spline for the smoothing kernel and an artificial viscosity prescription coupled with a Balsara Switch to prevent unphysical interparticle penetration. The code also implements an artificial relaxation force to the equations of motion to add a drag term to the calculated accelerations during relaxation integrations. Initially called StarCrash, StarSmasher was developed originally by Rasio.

Conservative, special-relativistic smoothed particle hydrodynamics

NASA Astrophysics Data System (ADS)

Rosswog, Stephan

2010-11-01

We present and test a new, special-relativistic formulation of smoothed particle hydrodynamics (SPH). Our approach benefits from several improvements with respect to earlier relativistic SPH formulations. It is self-consistently derived from the Lagrangian of an ideal fluid and accounts for the terms that stem from non-constant smoothing lengths, usually called “grad-h terms”. In our approach, we evolve the canonical momentum and the canonical energy per baryon and thus circumvent some of the problems that have plagued earlier formulations of relativistic SPH. We further use a much improved artificial viscosity prescription which uses the extreme local eigenvalues of the Euler equations and triggers selectively on (a) shocks and (b) velocity noise. The shock trigger accurately monitors the relative density slope and uses it to fine-tune the amount of artificial viscosity that is applied. This procedure substantially sharpens shock fronts while still avoiding post-shock noise. If not triggered, the viscosity parameter of each particle decays to zero. None of these viscosity triggers is specific to special relativity, both could also be applied in Newtonian SPH.The performance of the new scheme is explored in a large variety of benchmark tests where it delivers excellent results. Generally, the grad-h terms deliver minor, though worthwhile, improvements. As expected for a Lagrangian method, it performs close to perfect in supersonic advection tests, but also in strong relativistic shocks, usually considered a particular challenge for SPH, the method yields convincing results. For example, due to its perfect conservation properties, it is able to handle Lorentz factors as large as γ = 50,000 in the so-called wall shock test. Moreover, we find convincing results in a rarely shown, but challenging test that involves so-called relativistic simple waves and also in multi-dimensional shock tube tests.

The SPH consistency problem and some astrophysical applications

NASA Astrophysics Data System (ADS)

Klapp, Jaime; Sigalotti, Leonardo; Rendon, Otto; Gabbasov, Ruslan; Torres, Ayax

2017-11-01

We discuss the SPH kernel and particle consistency problem and demonstrate that SPH has a limiting second-order convergence rate. We also present a solution to the SPH consistency problem. We present examples of how SPH implementations that are not mathematically consistent may lead to erroneous results. The new formalism has been implemented into the Gadget 2 code, including an improved scheme for the artificial viscosity. We present results for the ``Standard Isothermal Test Case'' of gravitational collapse and fragmentation of protostellar molecular cores that produce a very different evolution than with the standard SPH theory. A further application of accretion onto a black hole is presented.

SPH simulation of turbulent flow past a high-frequency in-line oscillating cylinder near free-surface

NASA Astrophysics Data System (ADS)

Ghazanfarian, Jafar; Saghatchi, Roozbeh; Gorji-Bandpy, Mofid

2016-08-01

This paper studies a two-dimensional incompressible viscous flow past a circular cylinder with in-line oscillation close to a free-surface. The sub-particle scale (SPS) turbulence model of a Lagrangian particle-based smoothed-particle hydrodynamics (SPH) method has been used to solve the full Navier-Stokes equations together with the continuity equation. The accuracy of numerical code has been verified using two cases consisting of an oscillating cylinder placed in the stationary fluid, and flow over a fixed cylinder close to a free-surface. Simulations are conducted for the Froude number of 0.3, the Reynolds numbers of 40 and 80, various gap ratios for fully-submerged and half-submerge cylinders. The dimensionless frequency and amplitude of oscillating have been chosen as 0.5, 0.8 and 10, 15, respectively. The selection of such a high oscillating frequency causes the flow regime to become turbulent. It is seen that the gap ratio defined as the ratio of cylinder distance from free-surface and its diameter, strongly affects the flow pattern and the magnitude of the drag and lift coefficients. The jet-like flow (the region above the cylinder and beneath the free-surface) creation is discussed in detail and showed that the strength of this jet-like flow is weakened when the gap ratio shrinks. It is seen that by decreasing the gap ratio, the lift and drag coefficients increase and decrease, respectively. It is found that the Reynolds number has an inverse effect on the drag and lift coefficients. Also, it is concluded that by increasing the amplitude of oscillation the drag coefficient increases.

Modeling Water Waves with Smoothed Particle Hydrodynamics

DTIC Science & Technology

2011-09-30

Lagrangian nature of SPH allows the modeling of wave breaking, surf zones, ship waves, and wave-structure interaction, where the free surface becomes...particle detection--To study free surface flows and analyze their complex deformations, we need to know which particles are located on the free surface ...Hydrodynamics is proving to be a competent modeling scheme for free surface flows in two and three dimensions. As the GPU hardware improves, it is

Evaluating simulant materials for understanding cranial backspatter from a ballistic projectile.

PubMed

Das, Raj; Collins, Alistair; Verma, Anurag; Fernandez, Justin; Taylor, Michael

2015-05-01

In cranial wounds resulting from a gunshot, the study of backspatter patterns can provide information about the actual incidents by linking material to surrounding objects. This study investigates the physics of backspatter from a high-speed projectile impact and evaluates a range of simulant materials using impact tests. Next, we evaluate a mesh-free method called smoothed particle hydrodynamics (SPH) to model the splashing mechanism during backspatter. The study has shown that a projectile impact causes fragmentation at the impact site, while transferring momentum to fragmented particles. The particles travel along the path of least resistance, leading to partial material movement in the reverse direction of the projectile motion causing backspatter. Medium-density fiberboard is a better simulant for a human skull than polycarbonate, and lorica leather is a better simulant for a human skin than natural rubber. SPH is an effective numerical method for modeling the high-speed impact fracture and fragmentations. © 2015 American Academy of Forensic Sciences.

Multi-dimensional computer simulation of MHD combustor hydrodynamics

NASA Astrophysics Data System (ADS)

Berry, G. F.; Chang, S. L.; Lottes, S. A.; Rimkus, W. A.

1991-04-01

Argonne National Laboratory is investigating the nonreacting jet gas mixing patterns in an MHD second stage combustor by using a 2-D multiphase hydrodynamics computer program and a 3-D single phase hydrodynamics computer program. The computer simulations are intended to enhance the understanding of flow and mixing patterns in the combustor, which in turn may lead to improvement of the downstream MHD channel performance. A 2-D steady state computer model, based on mass and momentum conservation laws for multiple gas species, is used to simulate the hydrodynamics of the combustor in which a jet of oxidizer is injected into an unconfined cross stream gas flow. A 3-D code is used to examine the effects of the side walls and the distributed jet flows on the non-reacting jet gas mixing patterns. The code solves the conservation equations of mass, momentum, and energy, and a transport equation of a turbulence parameter and allows permeable surfaces to be specified for any computational cell.

Smoothed particle hydrodynamics study of the roughness effect on contact angle and droplet flow.

PubMed

Shigorina, Elena; Kordilla, Jannes; Tartakovsky, Alexandre M

2017-09-01

We employ a pairwise force smoothed particle hydrodynamics (PF-SPH) model to simulate sessile and transient droplets on rough hydrophobic and hydrophilic surfaces. PF-SPH allows modeling of free-surface flows without discretizing the air phase, which is achieved by imposing the surface tension and dynamic contact angles with pairwise interaction forces. We use the PF-SPH model to study the effect of surface roughness and microscopic contact angle on the effective contact angle and droplet dynamics. In the first part of this work, we investigate static contact angles of sessile droplets on different types of rough surfaces. We find that the effective static contact angles of Cassie and Wenzel droplets on a rough surface are greater than the corresponding microscale static contact angles. As a result, microscale hydrophobic rough surfaces also show effective hydrophobic behavior. On the other hand, microscale hydrophilic surfaces may be macroscopically hydrophilic or hydrophobic, depending on the type of roughness. We study the dependence of the transition between Cassie and Wenzel states on roughness and droplet size, which can be linked to the critical pressure for the given fluid-substrate combination. We observe good agreement between simulations and theoretical predictions. Finally, we study the impact of the roughness orientation (i.e., an anisotropic roughness) and surface inclination on droplet flow velocities. Simulations show that droplet flow velocities are lower if the surface roughness is oriented perpendicular to the flow direction. If the predominant elements of surface roughness are in alignment with the flow direction, the flow velocities increase compared to smooth surfaces, which can be attributed to the decrease in fluid-solid contact area similar to the lotus effect. We demonstrate that classical linear scaling relationships between Bond and capillary numbers for droplet flow on flat surfaces also hold for flow on rough surfaces.

Fluid-Structure Interaction Study of Transcatheter Aortic Valve Dynamics Using Smoothed Particle Hydrodynamics.

PubMed

Mao, Wenbin; Li, Kewei; Sun, Wei

2016-12-01

Computational modeling of heart valve dynamics incorporating both fluid dynamics and valve structural responses has been challenging. In this study, we developed a novel fully-coupled fluid-structure interaction (FSI) model using smoothed particle hydrodynamics (SPH). A previously developed nonlinear finite element (FE) model of transcatheter aortic valves (TAV) was utilized to couple with SPH to simulate valve leaflet dynamics throughout the entire cardiac cycle. Comparative simulations were performed to investigate the impact of using FE-only models vs. FSI models, as well as an isotropic vs. an anisotropic leaflet material model in TAV simulations. From the results, substantial differences in leaflet kinematics between FE-only and FSI models were observed, and the FSI model could capture the realistic leaflet dynamic deformation due to its more accurate spatial and temporal loading conditions imposed on the leaflets. The stress and the strain distributions were similar between the FE and FSI simulations. However, the peak stresses were different due to the water hammer effect induced by the fluid inertia in the FSI model during the closing phase, which led to 13-28% lower peak stresses in the FE-only model compared to that of the FSI model. The simulation results also indicated that tissue anisotropy had a minor impact on hemodynamics of the valve. However, a lower tissue stiffness in the radial direction of the leaflets could reduce the leaflet peak stress caused by the water hammer effect. It is hoped that the developed FSI models can serve as an effective tool to better assess valve dynamics and optimize next generation TAV designs.

NUMERICAL CONVERGENCE IN SMOOTHED PARTICLE HYDRODYNAMICS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Qirong; Li, Yuexing; Hernquist, Lars

2015-02-10

We study the convergence properties of smoothed particle hydrodynamics (SPH) using numerical tests and simple analytic considerations. Our analysis shows that formal numerical convergence is possible in SPH only in the joint limit N → ∞, h → 0, and N{sub nb} → ∞, where N is the total number of particles, h is the smoothing length, and N{sub nb} is the number of neighbor particles within the smoothing volume used to compute smoothed estimates. Previous work has generally assumed that the conditions N → ∞ and h → 0 are sufficient to achieve convergence, while holding N{sub nb} fixed.more » We demonstrate that if N{sub nb} is held fixed as the resolution is increased, there will be a residual source of error that does not vanish as N → ∞ and h → 0. Formal numerical convergence in SPH is possible only if N{sub nb} is increased systematically as the resolution is improved. Using analytic arguments, we derive an optimal compromise scaling for N{sub nb} by requiring that this source of error balance that present in the smoothing procedure. For typical choices of the smoothing kernel, we find N{sub nb} ∝N {sup 0.5}. This means that if SPH is to be used as a numerically convergent method, the required computational cost does not scale with particle number as O(N), but rather as O(N {sup 1} {sup +} {sup δ}), where δ ≈ 0.5, with a weak dependence on the form of the smoothing kernel.« less

Dusty gas with one fluid in smoothed particle hydrodynamics

NASA Astrophysics Data System (ADS)

Laibe, Guillaume; Price, Daniel J.

2014-05-01

In a companion paper we have shown how the equations describing gas and dust as two fluids coupled by a drag term can be re-formulated to describe the system as a single-fluid mixture. Here, we present a numerical implementation of the one-fluid dusty gas algorithm using smoothed particle hydrodynamics (SPH). The algorithm preserves the conservation properties of the SPH formalism. In particular, the total gas and dust mass, momentum, angular momentum and energy are all exactly conserved. Shock viscosity and conductivity terms are generalized to handle the two-phase mixture accordingly. The algorithm is benchmarked against a comprehensive suit of problems: DUSTYBOX, DUSTYWAVE, DUSTYSHOCK and DUSTYOSCILL, each of them addressing different properties of the method. We compare the performance of the one-fluid algorithm to the standard two-fluid approach. The one-fluid algorithm is found to solve both of the fundamental limitations of the two-fluid algorithm: it is no longer possible to concentrate dust below the resolution of the gas (they have the same resolution by definition), and the spatial resolution criterion h < csts, required in two-fluid codes to avoid over-damping of kinetic energy, is unnecessary. Implicit time-stepping is straightforward. As a result, the algorithm is up to ten billion times more efficient for 3D simulations of small grains. Additional benefits include the use of half as many particles, a single kernel and fewer SPH interpolations. The only limitation is that it does not capture multi-streaming of dust in the limit of zero coupling, suggesting that in this case a hybrid approach may be required.

Comparison of hydrodynamic simulations with two-shockwave drive target experiments

NASA Astrophysics Data System (ADS)

Karkhanis, Varad; Ramaprabhu, Praveen; Buttler, William

2015-11-01

We consider hydrodynamic continuum simulations to mimic ejecta generation in two-shockwave target experiments, where metallic surface is loaded by two successive shock waves. Time of second shock in simulations is determined to match experimental amplitudes at the arrival of the second shock. The negative Atwood number (A --> - 1) of ejecta simulations leads to two successive phase inversions of the interface corresponding to the passage of the shocks from heavy to light media in each instance. Metallic phase of ejecta (solid/liquid) depends on shock loading pressure in the experiment, and we find that hydrodynamic simulations quantify the liquid phase ejecta physics with a fair degree of accuracy, where RM instability is not suppressed by the strength effect. In particular, we find that our results of free surface velocity, maximum ejecta velocity, and maximum ejecta areal density are in excellent agreement with their experimental counterparts, as well as ejecta models. We also comment on the parametric space for hydrodynamic simulations in which they can be used to compare with the target experiments.

Parallel implementation of the particle simulation method with dynamic load balancing: Toward realistic geodynamical simulation

NASA Astrophysics Data System (ADS)

Furuichi, M.; Nishiura, D.

2015-12-01

Fully Lagrangian methods such as Smoothed Particle Hydrodynamics (SPH) and Discrete Element Method (DEM) have been widely used to solve the continuum and particles motions in the computational geodynamics field. These mesh-free methods are suitable for the problems with the complex geometry and boundary. In addition, their Lagrangian nature allows non-diffusive advection useful for tracking history dependent properties (e.g. rheology) of the material. These potential advantages over the mesh-based methods offer effective numerical applications to the geophysical flow and tectonic processes, which are for example, tsunami with free surface and floating body, magma intrusion with fracture of rock, and shear zone pattern generation of granular deformation. In order to investigate such geodynamical problems with the particle based methods, over millions to billion particles are required for the realistic simulation. Parallel computing is therefore important for handling such huge computational cost. An efficient parallel implementation of SPH and DEM methods is however known to be difficult especially for the distributed-memory architecture. Lagrangian methods inherently show workload imbalance problem for parallelization with the fixed domain in space, because particles move around and workloads change during the simulation. Therefore dynamic load balance is key technique to perform the large scale SPH and DEM simulation. In this work, we present the parallel implementation technique of SPH and DEM method utilizing dynamic load balancing algorithms toward the high resolution simulation over large domain using the massively parallel super computer system. Our method utilizes the imbalances of the executed time of each MPI process as the nonlinear term of parallel domain decomposition and minimizes them with the Newton like iteration method. In order to perform flexible domain decomposition in space, the slice-grid algorithm is used. Numerical tests show that our

PowderSim: Lagrangian Discrete and Mesh-Free Continuum Simulation Code for Cohesive Soils

NASA Technical Reports Server (NTRS)

Johnson, Scott; Walton, Otis; Settgast, Randolph

2013-01-01

PowderSim is a calculation tool that combines a discrete-element method (DEM) module, including calibrated interparticle-interaction relationships, with a mesh-free, continuum, SPH (smoothed-particle hydrodynamics) based module that utilizes enhanced, calibrated, constitutive models capable of mimicking both large deformations and the flow behavior of regolith simulants and lunar regolith under conditions anticipated during in situ resource utilization (ISRU) operations. The major innovation introduced in PowderSim is to use a mesh-free method (SPH-based) with a calibrated and slightly modified critical-state soil mechanics constitutive model to extend the ability of the simulation tool to also address full-scale engineering systems in the continuum sense. The PowderSim software maintains the ability to address particle-scale problems, like size segregation, in selected regions with a traditional DEM module, which has improved contact physics and electrostatic interaction models.

Hydrodynamic Simulations of Protoplanetary Disks with GIZMO

NASA Astrophysics Data System (ADS)

Rice, Malena; Laughlin, Greg

2018-01-01

Over the past several decades, the field of computational fluid dynamics has rapidly advanced as the range of available numerical algorithms and computationally feasible physical problems has expanded. The development of modern numerical solvers has provided a compelling opportunity to reconsider previously obtained results in search for yet undiscovered effects that may be revealed through longer integration times and more precise numerical approaches. In this study, we compare the results of past hydrodynamic disk simulations with those obtained from modern analytical resources. We focus our study on the GIZMO code (Hopkins 2015), which uses meshless methods to solve the homogeneous Euler equations of hydrodynamics while eliminating problems arising as a result of advection between grid cells. By comparing modern simulations with prior results, we hope to provide an improved understanding of the impact of fluid mechanics upon the evolution of protoplanetary disks.

Smoothed particle hydrodynamic modeling of volcanic debris flows: Application to Huiloac Gorge lahars (Popocatépetl volcano, Mexico)

NASA Astrophysics Data System (ADS)

Haddad, Bouchra; Palacios, David; Pastor, Manuel; Zamorano, José Juan

2016-09-01

Lahars are among the most catastrophic volcanic processes, and the ability to model them is central to mitigating their effects. Several lahars recently generated by the Popocatépetl volcano (Mexico) moved downstream through the Huiloac Gorge towards the village of Santiago Xalitzintla. The most dangerous was the 2001 lahar, in which the destructive power of the debris flow was maintained throughout the extent of the flow. Identifying the zone of hazard can be based either on numerical or empirical models, but a calibration and validation process is required to ensure hazard map quality. The Geoflow-SPH depth integrated numerical model used in this study to reproduce the 2001 lahar was derived from the velocity-pressure version of the Biot-Zienkiewicz model, and was discretized using the smoothed particle hydrodynamics (SPH) method. The results of the calibrated SPH model were validated by comparing the simulated deposit depth with the field depth measured at 16 cross sections distributed strategically along the gorge channel. Moreover, the dependency of the results on topographic mesh resolution, initial lahar mass shape and dimensions is also investigated. The results indicate that to accurately reproduce the 2001 lahar flow dynamics the channel topography needed to be discretized using a mesh having a minimum 5 m resolution, and an initial lahar mass shape that adopted the source area morphology. Field validation of the calibrated model showed that there was a satisfactory relationship between the simulated and field depths, the error being less than 20% for 11 of the 16 cross sections. This study demonstrates that the Geoflow-SPH model was able to accurately reproduce the lahar path and the extent of the flow, but also reproduced other parameters including flow velocity and deposit depth.

Core-Collapse Supernovae Explored by Multi-D Boltzmann Hydrodynamic Simulations

NASA Astrophysics Data System (ADS)

Sumiyoshi, Kohsuke; Nagakura, Hiroki; Iwakami, Wakana; Furusawa, Shun; Matsufuru, Hideo; Imakura, Akira; Yamada, Shoichi

We report the latest results of numerical simulations of core-collapse supernovae by solving multi-D neutrino-radiation hydrodynamics with Boltzmann equations. One of the longstanding issues of the explosion mechanism of supernovae has been uncertainty in the approximations of the neutrino transfer in multi-D such as the diffusion approximation and ray-by-ray method. The neutrino transfer is essential, together with 2D/3D hydrodynamical instabilities, to evaluate the neutrino heating behind the shock wave for successful explosions and to predict the neutrino burst signals. We tackled this difficult problem by utilizing our solver of the 6D Boltzmann equation for neutrinos in 3D space and 3D neutrino momentum space coupled with multi-D hydrodynamics adding special and general relativistic extensions. We have performed a set of 2D core-collapse simulations from 11M ⊙ and 15M ⊙ stars on K-computer in Japan by following long-term evolution over 400 ms after bounce to reveal the outcome from the full Boltzmann hydrodynamic simulations with a sophisticated equation of state with multi-nuclear species and updated rates for electron captures on nuclei.

A full scale hydrodynamic simulation of pyrotechnic combustion

NASA Astrophysics Data System (ADS)

Kim, Bohoon; Jang, Seung-Gyo; Yoh, Jack

2017-06-01

A full scale hydrodynamic simulation that requires an accurate reproduction of shock-induced detonation was conducted for design of an energetic component system. A series of small scale gap tests and detailed hydrodynamic simulations were used to validate the reactive flow model for predicting the shock propagation in a train configuration and to quantify the shock sensitivity of the energetic materials. The energetic component system is composed of four main components, namely a donor unit (HNS + HMX), a bulkhead (STS), an acceptor explosive (RDX), and a propellant (BKNO3) for gas generation. The pressurized gases generated from the burning propellant were purged into a 10 cc release chamber for study of the inherent oscillatory flow induced by the interferences between shock and rarefaction waves. The pressure fluctuations measured from experiment and calculation were investigated to further validate the peculiar peak at specific characteristic frequency (ωc = 8.3 kHz). In this paper, a step-by-step numerical description of detonation of high explosive components, deflagration of propellant component, and deformation of metal component is given in order to facilitate the proper implementation of the outlined formulation into a shock physics code for a full scale hydrodynamic simulation of the energetic component system.

Smoothed-particle-hydrodynamics modeling of dissipation mechanisms in gravity waves.

PubMed

Colagrossi, Andrea; Souto-Iglesias, Antonio; Antuono, Matteo; Marrone, Salvatore

2013-02-01

The smoothed-particle-hydrodynamics (SPH) method has been used to study the evolution of free-surface Newtonian viscous flows specifically focusing on dissipation mechanisms in gravity waves. The numerical results have been compared with an analytical solution of the linearized Navier-Stokes equations for Reynolds numbers in the range 50-5000. We found that a correct choice of the number of neighboring particles is of fundamental importance in order to obtain convergence towards the analytical solution. This number has to increase with higher Reynolds numbers in order to prevent the onset of spurious vorticity inside the bulk of the fluid, leading to an unphysical overdamping of the wave amplitude. This generation of spurious vorticity strongly depends on the specific kernel function used in the SPH model.

Evolution of Occupant Survivability Simulation Framework Using FEM-SPH Coupling

DTIC Science & Technology

2011-08-01

SPH Coupling, Dooge and Thyagarajan. UNCLASSIFIED: Dist A. Approved for public release Page 2 of 14 works outward in the chain: soldier  seats ...reduced degree of freedom (DOF) system, evaluation of occupant seating independent of the vehicle environment, or using a substructure approach to...the ejected material covering the charge imposes most of the loading onto the structure above. The properties of the material in the "soil cap" are

Fluid-structure interaction study of transcatheter aortic valve dynamics using smoothed particle hydrodynamics

PubMed Central

Mao, Wenbin; Li, Kewei; Sun, Wei

2016-01-01

Computational modeling of heart valve dynamics incorporating both fluid dynamics and valve structural responses has been challenging. In this study, we developed a novel fully-coupled fluid-structure interaction (FSI) model using smoothed particle hydrodynamics (SPH). A previously developed nonlinear finite element (FE) model of transcatheter aortic valves (TAV) was utilized to couple with SPH to simulate valve leaflet dynamics throughout the entire cardiac cycle. Comparative simulations were performed to investigate the impact of using FE-only models versus FSI models, as well as an isotropic versus an anisotropic leaflet material model in TAV simulations. From the results, substantial differences in leaflet kinematics between FE-only and FSI models were observed, and the FSI model could capture the realistic leaflet dynamic deformation due to its more accurate spatial and temporal loading conditions imposed on the leaflets. The stress and the strain distributions were similar between the FE and FSI simulations. However, the peak stresses were different due to the water hammer effect induced by the flow inertia in the FSI model during the closing phase, which led to 13%–28% lower peak stresses in the FE-only model compared to that of the FSI model. The simulation results also indicated that tissue anisotropy had a minor impact on hemodynamics of the valve. However, a lower tissue stiffness in the radial direction of the leaflets could reduce the leaflet peak stress caused by the water hammer effect. It is hoped that the developed FSI models can serve as an effective tool to better assess valve dynamics and optimize next generation TAV designs. PMID:27844463

SPH for impact force and ricochet behavior of water-entry bodies

NASA Astrophysics Data System (ADS)

Omidvar, Pourya; Farghadani, Omid; Nikeghbali, Pooyan

The numerical modeling of fluid interaction with a bouncing body has many applications in scientific and engineering application. In this paper, the problem of water impact of a body on free-surface is investigated, where the fixed ghost boundary condition is added to the open source code SPHysics2D1 to rectify the oscillations in pressure distributions with the repulsive boundary condition. First, after introducing the methodology of SPH and the option of boundary conditions, the still water problem is simulated using two types of boundary conditions. It is shown that the fixed ghost boundary condition gives a better result for a hydrostatics pressure. Then, the dam-break problem, which is a bench mark test case in SPH, is simulated and compared with available data. In order to show the behavior of the hydrostatics forces on bodies, a fix/floating cylinder is placed on free surface looking carefully at the force and heaving profile. Finally, the impact of a body on free-surface is successfully simulated for different impact angles and velocities.

Development of a two-phase SPH model for sediment laden flows

NASA Astrophysics Data System (ADS)

Shi, Huabin; Yu, Xiping; Dalrymple, Robert A.

2017-12-01

A SPH model based on a general formulation for solid-fluid two-phase flows is proposed for suspended sediment motion in free surface flows. The water and the sediment are treated as two miscible fluids, and the multi-fluid system is discretized by a single set of SPH particles, which move with the water velocity and carry properties of the two phases. Large eddy simulation (LES) is introduced to deal with the turbulence effect, and the widely used Smagorinsky model is modified to take into account the influence of sediment particles on the turbulence. The drag force is accurately formulated by including the hindered settling effect. In the model, the water is assumed to be weakly compressible while the sediment is incompressible, and a new equation of state is proposed for the pressure in the sediment-water mixture. Dynamic boundary condition is employed to treat wall boundaries, and a new strategy of Shepard filtering is adopted to damp the pressure oscillation. The developed two-phase SPH model is validated by comparing the numerical results with analytical solutions for idealized cases of still water containing both neutrally buoyant and naturally settling sand and for plane Poiseuille flows carrying neutrally buoyant particles, and is then applied to sand dumping from a line source into a water tank, where the sand cloud settles with a response of the free water surface. It is shown that the numerical results are in good agreement with the experimental data as well as the empirical formulas. The characteristics of the settling sand cloud, the pressure field, and the flow vortices are studied. The motion of the free water surface is also discussed. The proposed two-phase SPH model is proven to be effective for numerical simulation of sand dumping into waters.

Comparison of hydrodynamic simulations with two-shockwave drive target experiments

NASA Astrophysics Data System (ADS)

Karkhanis, Varad; Ramaprabhu, Praveen; Buttler, William

2015-11-01

We consider hydrodynamic continuum simulations to mimic ejecta generation in two-shockwave target experiments, where metallic surface is loaded by two successive shock waves. Time of second shock in simulations is determined to match experimental amplitudes at the arrival of the second shock. The negative Atwood number A --> - 1 of ejecta simulations leads to two successive phase inversions of the interface corresponding to the passage of the shocks from heavy to light media in each instance. Metallic phase of ejecta (solid/liquid) depends on shock loading pressure in the experiment, and we find that hydrodynamic simulations quantify the liquid phase ejecta physics with a fair degree of accuracy, where RM instability is not suppressed by the strength effect. In particular, we find that our results of free surface velocity, maximum ejecta velocity, and maximum ejecta areal density are in excellent agreement with their experimental counterparts, as well as ejecta models. We also comment on the parametric space for hydrodynamic simulations in which they can be used to compare with the target experiments. This work was supported in part by the (U.S.) Department of Energy (DOE) under Contract No. DE-AC52-06NA2-5396.

A method of smoothed particle hydrodynamics using spheroidal kernels

NASA Technical Reports Server (NTRS)

Fulbright, Michael S.; Benz, Willy; Davies, Melvyn B.

1995-01-01

We present a new method of three-dimensional smoothed particle hydrodynamics (SPH) designed to model systems dominated by deformation along a preferential axis. These systems cause severe problems for SPH codes using spherical kernels, which are best suited for modeling systems which retain rough spherical symmetry. Our method allows the smoothing length in the direction of the deformation to evolve independently of the smoothing length in the perpendicular plane, resulting in a kernel with a spheroidal shape. As a result the spatial resolution in the direction of deformation is significantly improved. As a test case we present the one-dimensional homologous collapse of a zero-temperature, uniform-density cloud, which serves to demonstrate the advantages of spheroidal kernels. We also present new results on the problem of the tidal disruption of a star by a massive black hole.

A web portal for hydrodynamical, cosmological simulations

NASA Astrophysics Data System (ADS)

Ragagnin, A.; Dolag, K.; Biffi, V.; Cadolle Bel, M.; Hammer, N. J.; Krukau, A.; Petkova, M.; Steinborn, D.

2017-07-01

This article describes a data centre hosting a web portal for accessing and sharing the output of large, cosmological, hydro-dynamical simulations with a broad scientific community. It also allows users to receive related scientific data products by directly processing the raw simulation data on a remote computing cluster. The data centre has a multi-layer structure: a web portal, a job control layer, a computing cluster and a HPC storage system. The outer layer enables users to choose an object from the simulations. Objects can be selected by visually inspecting 2D maps of the simulation data, by performing highly compounded and elaborated queries or graphically by plotting arbitrary combinations of properties. The user can run analysis tools on a chosen object. These services allow users to run analysis tools on the raw simulation data. The job control layer is responsible for handling and performing the analysis jobs, which are executed on a computing cluster. The innermost layer is formed by a HPC storage system which hosts the large, raw simulation data. The following services are available for the users: (I) CLUSTERINSPECT visualizes properties of member galaxies of a selected galaxy cluster; (II) SIMCUT returns the raw data of a sub-volume around a selected object from a simulation, containing all the original, hydro-dynamical quantities; (III) SMAC creates idealized 2D maps of various, physical quantities and observables of a selected object; (IV) PHOX generates virtual X-ray observations with specifications of various current and upcoming instruments.

Comparison of Non-Parabolic Hydrodynamic Simulations for Semiconductor Devices

NASA Technical Reports Server (NTRS)

Smith, A. W.; Brennan, K. F.

1996-01-01

Parabolic drift-diffusion simulators are common engineering level design tools for semiconductor devices. Hydrodynamic simulators, based on the parabolic band approximation, are becoming more prevalent as device dimensions shrink and energy transport effects begin to dominate device characteristic. However, band structure effects present in state-of-the-art devices necessitate relaxing the parabolic band approximation. This paper presents simulations of ballistic diodes, a benchmark device, of Si and GaAs using two different non-parabolic hydrodynamic formulations. The first formulation uses the Kane dispersion relationship in the derivation of the conservation equations. The second model uses a power law dispersion relation {(hk)(exp 2)/2m = xW(exp Y)}. Current-voltage relations show that for the ballistic diodes considered. the non-parabolic formulations predict less current than the parabolic case. Explanations of this will be provided by examination of velocity and energy profiles. At low bias, the simulations based on the Kane formulation predict greater current flow than the power law formulation. As the bias is increased this trend changes and the power law predicts greater current than the Kane formulation. It will be shown that the non-parabolicity and energy range of the hydrodynamic model based on the Kane dispersion relation are limited due to the binomial approximation which was utilized in the derivation.

Smoothed particle hydrodynamics study of the roughness effect on contact angle and droplet flow

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shigorina, Elena; Kordilla, Jannes; Tartakovsky, Alexandre M.

We employ a pairwise force Smoothed Particle Hydrodynamics (PF-SPH) model to simulate sessile and transient droplets on rough hydrophobic and hydrophilic surfaces. PF-SPH allows for modeling of free surface flow without discretizing the air phase, which is achieved by imposing the surface tension and dynamic contact angles with pairwise interaction forces. We use the PF-SPH model to study the effect of surface roughness and microscopic contact angle on the effective contact angle and droplet dynamics. In the first part of this work, we investigate static contact angles of sessile droplets on rough surfaces in a shape of a sinusoidal functionmore » and made of rectangular bars placed on top of a flat surface. We find that the effective static contact angles of Cassie and Wenzel droplets on a rough surface are greater than the corresponding microscale static contact angles. As a result, microscale hydrophobic rough surfaces also show effective hydrophobic behavior. On the other hand, microscale hydrophilic surfaces may be macroscopically hydrophilic or hydrophobic, depending on the type of roughness. Next, we study the impact of the roughness orientation (i.e., an anisotropic roughness) and surface inclination on droplet flow velocities. Simulations show that droplet flow velocities are lower if the surface roughness is oriented perpendicular to the flow direction. If the predominant elements of surface roughness are in alignment with the flow direction, the flow velocities increase compared to smooth surfaces, which can be attributed to the decrease in fluid-solid contact area similar to the classical lotus effect. We demonstrate that linear scaling relationships between Bond and capillary number for droplet flow on flat surfaces also hold for flow on rough surfaces.« less

An iterative method for hydrodynamic interactions in Brownian dynamics simulations of polymer dynamics

NASA Astrophysics Data System (ADS)

Miao, Linling; Young, Charles D.; Sing, Charles E.

2017-07-01

Brownian Dynamics (BD) simulations are a standard tool for understanding the dynamics of polymers in and out of equilibrium. Quantitative comparison can be made to rheological measurements of dilute polymer solutions, as well as direct visual observations of fluorescently labeled DNA. The primary computational challenge with BD is the expensive calculation of hydrodynamic interactions (HI), which are necessary to capture physically realistic dynamics. The full HI calculation, performed via a Cholesky decomposition every time step, scales with the length of the polymer as O(N3). This limits the calculation to a few hundred simulated particles. A number of approximations in the literature can lower this scaling to O(N2 - N2.25), and explicit solvent methods scale as O(N); however both incur a significant constant per-time step computational cost. Despite this progress, there remains a need for new or alternative methods of calculating hydrodynamic interactions; large polymer chains or semidilute polymer solutions remain computationally expensive. In this paper, we introduce an alternative method for calculating approximate hydrodynamic interactions. Our method relies on an iterative scheme to establish self-consistency between a hydrodynamic matrix that is averaged over simulation and the hydrodynamic matrix used to run the simulation. Comparison to standard BD simulation and polymer theory results demonstrates that this method quantitatively captures both equilibrium and steady-state dynamics after only a few iterations. The use of an averaged hydrodynamic matrix allows the computationally expensive Brownian noise calculation to be performed infrequently, so that it is no longer the bottleneck of the simulation calculations. We also investigate limitations of this conformational averaging approach in ring polymers.

Simulating X-ray bursts with a radiation hydrodynamics code

NASA Astrophysics Data System (ADS)

Seong, Gwangeon; Kwak, Kyujin

2018-04-01

Previous simulations of X-ray bursts (XRBs), for example, those performed by MESA (Modules for Experiments in Stellar Astrophysics) could not address the dynamical effects of strong radiation, which are important to explain the photospheric radius expansion (PRE) phenomena seen in many XRBs. In order to study the effects of strong radiation, we propose to use SNEC (the SuperNova Explosion Code), a 1D Lagrangian open source code that is designed to solve hydrodynamics and equilibrium-diffusion radiation transport together. Because SNEC is able to control modules of radiation-hydrodynamics for properly mapped inputs, radiation-dominant pressure occurring in PRE XRBs can be handled. Here we present simulation models for PRE XRBs by applying SNEC together with MESA.

Hydrodynamically Coupled Brownian Dynamics: A coarse-grain particle-based Brownian dynamics technique with hydrodynamic interactions for modeling self-developing flow of polymer solutions

NASA Astrophysics Data System (ADS)

Ahuja, V. R.; van der Gucht, J.; Briels, W. J.

2018-01-01

We present a novel coarse-grain particle-based simulation technique for modeling self-developing flow of dilute and semi-dilute polymer solutions. The central idea in this paper is the two-way coupling between a mesoscopic polymer model and a phenomenological fluid model. As our polymer model, we choose Responsive Particle Dynamics (RaPiD), a Brownian dynamics method, which formulates the so-called "conservative" and "transient" pair-potentials through which the polymers interact besides experiencing random forces in accordance with the fluctuation dissipation theorem. In addition to these interactions, our polymer blobs are also influenced by the background solvent velocity field, which we calculate by solving the Navier-Stokes equation discretized on a moving grid of fluid blobs using the Smoothed Particle Hydrodynamics (SPH) technique. While the polymers experience this frictional force opposing their motion relative to the background flow field, our fluid blobs also in turn are influenced by the motion of the polymers through an interaction term. This makes our technique a two-way coupling algorithm. We have constructed this interaction term in such a way that momentum is conserved locally, thereby preserving long range hydrodynamics. Furthermore, we have derived pairwise fluctuation terms for the velocities of the fluid blobs using the Fokker-Planck equation, which have been alternatively derived using the General Equation for the Non-Equilibrium Reversible-Irreversible Coupling (GENERIC) approach in Smoothed Dissipative Particle Dynamics (SDPD) literature. These velocity fluctuations for the fluid may be incorporated into the velocity updates for our fluid blobs to obtain a thermodynamically consistent distribution of velocities. In cases where these fluctuations are insignificant, however, these additional terms may well be dropped out as they are in a standard SPH simulation. We have applied our technique to study the rheology of two different

Hydrodynamically Coupled Brownian Dynamics: A coarse-grain particle-based Brownian dynamics technique with hydrodynamic interactions for modeling self-developing flow of polymer solutions.

PubMed

Ahuja, V R; van der Gucht, J; Briels, W J

2018-01-21

We present a novel coarse-grain particle-based simulation technique for modeling self-developing flow of dilute and semi-dilute polymer solutions. The central idea in this paper is the two-way coupling between a mesoscopic polymer model and a phenomenological fluid model. As our polymer model, we choose Responsive Particle Dynamics (RaPiD), a Brownian dynamics method, which formulates the so-called "conservative" and "transient" pair-potentials through which the polymers interact besides experiencing random forces in accordance with the fluctuation dissipation theorem. In addition to these interactions, our polymer blobs are also influenced by the background solvent velocity field, which we calculate by solving the Navier-Stokes equation discretized on a moving grid of fluid blobs using the Smoothed Particle Hydrodynamics (SPH) technique. While the polymers experience this frictional force opposing their motion relative to the background flow field, our fluid blobs also in turn are influenced by the motion of the polymers through an interaction term. This makes our technique a two-way coupling algorithm. We have constructed this interaction term in such a way that momentum is conserved locally, thereby preserving long range hydrodynamics. Furthermore, we have derived pairwise fluctuation terms for the velocities of the fluid blobs using the Fokker-Planck equation, which have been alternatively derived using the General Equation for the Non-Equilibrium Reversible-Irreversible Coupling (GENERIC) approach in Smoothed Dissipative Particle Dynamics (SDPD) literature. These velocity fluctuations for the fluid may be incorporated into the velocity updates for our fluid blobs to obtain a thermodynamically consistent distribution of velocities. In cases where these fluctuations are insignificant, however, these additional terms may well be dropped out as they are in a standard SPH simulation. We have applied our technique to study the rheology of two different

Kinetic simulation of hydrodynamic equivalent capsule implosions

NASA Astrophysics Data System (ADS)

Kwan, Thomas; Le, Ari; Schmitt, Mark; Herrmann, Hans

2016-10-01

We have carried out simulations of direct-drive hydrodynamic equivalent capsule implosion experiments conducted on Omega laser facility at the Laboratory of Laser Energetics of the University of Rochester. The capsules had a glass shell (SiO2) 4.87 μm with an inner diameter of 1086 μm. One was filled with deuterium (D) and tritium (T) at 6.635 and 2.475 atmospheric pressure respectively. The other capsule with D, T, and He-3 at 2.475, 2.475, and 5.55 atmospheric pressure respectively. The capsules were imploded with 60 laser beams with a square pulse length of 0.6ns of total energy of 15.6 kJ. One-dimensional radiation hydrodynamic calculations with HYDRA and kinetic particle/hybrid simulations with LSP are carried out for the post-shot analysis. HYDRA outputs at 0.6ns are linked to LSP, in which the electrons are treated as a fluid while all the ion dynamics is simulated by the standard particle-in-cell technique. Additionally, simulations with the new photon package in LSP are initiated at the beginning of the implosion to include the implosion phase of the capsule. The simulation results of density, temperature, and velocity profiles of the electrons, D, T, He-3, and SiO2species are compared with HYDRA. Detail comparisons among the kinetic simulations, rad-hydro simulations, and experimental results of neutron yield, yield ratio, fusion burn histories, and shell convergence will be presented to assess plasma kinetic effects. Work performed under the auspices of the US DOE by the Los Alamos National Laboratory under Contract No. W7405-ENG-36.

MUFASA: galaxy formation simulations with meshless hydrodynamics

NASA Astrophysics Data System (ADS)

Davé, Romeel; Thompson, Robert; Hopkins, Philip F.

2016-11-01

We present the MUFASA suite of cosmological hydrodynamic simulations, which employs the GIZMO meshless finite mass (MFM) code including H2-based star formation, nine-element chemical evolution, two-phase kinetic outflows following scalings from the Feedback in Realistic Environments zoom simulations, and evolving halo mass-based quenching. Our fiducial (50 h-1 Mpc)3 volume is evolved to z = 0 with a quarter billion elements. The predicted galaxy stellar mass functions (GSMFs) reproduces observations from z = 4 → 0 to ≲ 1.2σ in cosmic variance, providing an unprecedented match to this key diagnostic. The cosmic star formation history and stellar mass growth show general agreement with data, with a strong archaeological downsizing trend such that dwarf galaxies form the majority of their stars after z ˜ 1. We run 25 and 12.5 h-1 Mpc volumes to z = 2 with identical feedback prescriptions, the latter resolving all hydrogen-cooling haloes, and the three runs display fair resolution convergence. The specific star formation rates broadly agree with data at z = 0, but are underpredicted at z ˜ 2 by a factor of 3, re-emphasizing a longstanding puzzle in galaxy evolution models. We compare runs using MFM and two flavours of smoothed particle hydrodynamics, and show that the GSMF is sensitive to hydrodynamics methodology at the ˜×2 level, which is sub-dominant to choices for parametrizing feedback.

Non-Parabolic Hydrodynamic Formulations for the Simulation of Inhomogeneous Semiconductor Devices

NASA Technical Reports Server (NTRS)

Smith, A. W.; Brennan, K. F.

1996-01-01

Hydrodynamic models are becoming prevalent design tools for small scale devices and other devices in which high energy effects can dominate transport. Most current hydrodynamic models use a parabolic band approximation to obtain fairly simple conservation equations. Interest in accounting for band structure effects in hydrodynamic device simulation has begun to grow since parabolic models cannot fully describe the transport in state of the art devices due to the distribution populating non-parabolic states within the band. This paper presents two different non-parabolic formulations or the hydrodynamic model suitable for the simulation of inhomogeneous semiconductor devices. The first formulation uses the Kane dispersion relationship ((hk)(exp 2)/2m = W(1 + alphaW). The second formulation makes use of a power law ((hk)(exp 2)/2m = xW(exp y)) for the dispersion relation. Hydrodynamic models which use the first formulation rely on the binomial expansion to obtain moment equations with closed form coefficients. This limits the energy range over which the model is valid. The power law formulation readily produces closed form coefficients similar to those obtained using the parabolic band approximation. However, the fitting parameters (x,y) are only valid over a limited energy range. The physical significance of the band non-parabolicity is discussed as well as the advantages/disadvantages and approximations of the two non-parabolic models. A companion paper describes device simulations based on the three dispersion relationships; parabolic, Kane dispersion and power law dispersion.

Non-parabolic hydrodynamic formulations for the simulation of inhomogeneous semiconductor devices

NASA Technical Reports Server (NTRS)

Smith, Arlynn W.; Brennan, Kevin F.

1995-01-01

Hydrodynamic models are becoming prevalent design tools for small scale devices and other devices in which high energy effects can dominate transport. Most current hydrodynamic models use a parabolic band approximation to obtain fairly simple conservation equations. Interest in accounting for band structure effects in hydrodynamic device simulation has begun to grow since parabolic models can not fully describe the transport in state of the art devices due to the distribution populating non-parabolic states within the band. This paper presents two different non-parabolic formulations of the hydrodynamic model suitable for the simulation of inhomogeneous semiconductor devices. The first formulation uses the Kane dispersion relationship (hk)(exp 2)/2m = W(1 + alpha(W)). The second formulation makes use of a power law ((hk)(exp 2)/2m = xW(sup y)) for the dispersion relation. Hydrodynamic models which use the first formulation rely on the binomial expansion to obtain moment equations with closed form coefficients. This limits the energy range over which the model is valid. The power law formulation readily produces closed form coefficients similar to those obtained using the parabolic band approximation. However, the fitting parameters (x,y) are only valid over a limited energy range. The physical significance of the band non-parabolicity is discussed as well as the advantages/disadvantages and approximations of the two non-parabolic models. A companion paper describes device simulations based on the three dispersion relationships: parabolic, Kane dispersion, and power low dispersion.

High-speed water impacts of flat plates in different ditching configuration through a Riemann-ALE SPH model

NASA Astrophysics Data System (ADS)

Marrone, S.; Colagrossi, A.; Chiron, L.; De Leffe, M.; Le Touzé, D.

2018-02-01

The violent water entry of flat plates is investigated using a Riemann-arbitrary Eulerian-Lagrangian (ALE) smoothed particle hydrodynamics (SPH) model. The test conditions are of interest for problems related to aircraft and helicopter emergency landing in water. Three main parameters are considered: the horizontal velocity, the approach angle (i.e., vertical to horizontal velocity ratio) and the pitch angle, α. Regarding the latter, small angles are considered in this study. As described in the theoretical work by Zhao and Faltinsen (1993), for small α a very thin, high-speed jet of water is formed, and the time-spatial gradients of the pressure field are extremely high. These test conditions are very challenging for numerical solvers. In the present study an enhanced SPH model is firstly tested on a purely vertical impact with deadrise angle α = 4°. An in-depth validation against analytical solutions and experimental results is carried out, highlighting the several critical aspects of the numerical modelling of this kind of flow, especially when pressure peaks are to be captured. A discussion on the main difficulties when comparing to model scale experiments is also provided. Then, the more realistic case of a plate with both horizontal and vertical velocity components is discussed and compared to ditching experiments recently carried out at CNR-INSEAN. In the latter case both 2-D and 3-D simulations are considered and the importance of 3-D effects on the pressure peak is discussed for α = 4° and α = 10°.

Mesoscale simulations of hydrodynamic squirmer interactions.

PubMed

Götze, Ingo O; Gompper, Gerhard

2010-10-01

The swimming behavior of self-propelled microorganisms is studied by particle-based mesoscale simulations. The simulation technique includes both hydrodynamics and thermal fluctuations that are both essential for the dynamics of microswimmers. The swimmers are modeled as squirmers, i.e., spherical objects with a prescribed tangential surface velocity, where the focus of thrust generation can be tuned from pushers to pullers. For passive squirmers (colloids), we show that the velocity autocorrelation function agrees quantitatively with the Boussinesq approximation. Single active squirmers show a persistent random-walk behavior, determined by forward motion, lateral diffusion, and orientational fluctuations, in agreement with theoretical predictions. For pairs of squirmers, which are initially swimming in parallel, we find an attraction for pushers and a repulsion for pullers, as expected. The hydrodynamic force between squirmer pairs is calculated as a function of the center-to-center distances d(cm) and is found to be consistent with a logarithmic distance dependence for d(cm) less than about two sphere diameters; here, the force is considerably stronger than expected from the far-field expansion. The dependence of the force strength on the asymmetry of the polar surface velocity is obtained. During the collision process, thermal fluctuations turn out to be very important and to strongly affect the postcollision velocity directions of both squirmers.

HYDRODYNAMIC SIMULATION OF THE UPPER POTOMAC ESTUARY.

USGS Publications Warehouse

Schaffranck, Raymond W.

1986-01-01

Hydrodynamics of the upper extent of the Potomac Estuary between Indian Head and Morgantown, Md. , are simulated using a two-dimensional model. The model computes water-surface elevations and depth-averaged velocities by numerically integrating finite-difference forms of the equations of mass and momentum conservation using the alternating direction implicit method. The fundamental, non-linear, unsteady-flow equations, upon which the model is formulated, include additional terms to account for Coriolis acceleration and meteorological influences. Preliminary model/prototype data comparisons show agreement to within 9% for tidal flow volumes and phase differences within the measured-data-recording interval. Use of the model to investigate the hydrodynamics and certain aspects of transport within this Potomac Estuary reach is demonstrated. Refs.

Hydrodynamic Simulations and Tomographic Reconstructions of the Intergalactic Medium

NASA Astrophysics Data System (ADS)

Stark, Casey William

The Intergalactic Medium (IGM) is the dominant reservoir of matter in the Universe from which the cosmic web and galaxies form. The structure and physical state of the IGM provides insight into the cosmological model of the Universe, the origin and timeline of the reionization of the Universe, as well as being an essential ingredient in our understanding of galaxy formation and evolution. Our primary handle on this information is a signal known as the Lyman-alpha forest (or Ly-alpha forest) -- the collection of absorption features in high-redshift sources due to intervening neutral hydrogen, which scatters HI Ly-alpha photons out of the line of sight. The Ly-alpha forest flux traces density fluctuations at high redshift and at moderate overdensities, making it an excellent tool for mapping large-scale structure and constraining cosmological parameters. Although the computational methodology for simulating the Ly-alpha forest has existed for over a decade, we are just now approaching the scale of computing power required to simultaneously capture large cosmological scales and the scales of the smallest absorption systems. My thesis focuses on using simulations at the edge of modern computing to produce precise predictions of the statistics of the Ly-alpha forest and to better understand the structure of the IGM. In the first part of my thesis, I review the state of hydrodynamic simulations of the IGM, including pitfalls of the existing under-resolved simulations. Our group developed a new cosmological hydrodynamics code to tackle the computational challenge, and I developed a distributed analysis framework to compute flux statistics from our simulations. I present flux statistics derived from a suite of our large hydrodynamic simulations and demonstrate convergence to the per cent level. I also compare flux statistics derived from simulations using different discretizations and hydrodynamic schemes (Eulerian finite volume vs. smoothed particle hydrodynamics) and

Testing hydrodynamics schemes in galaxy disc simulations

NASA Astrophysics Data System (ADS)

Few, C. G.; Dobbs, C.; Pettitt, A.; Konstandin, L.

2016-08-01

We examine how three fundamentally different numerical hydrodynamics codes follow the evolution of an isothermal galactic disc with an external spiral potential. We compare an adaptive mesh refinement code (RAMSES), a smoothed particle hydrodynamics code (SPHNG), and a volume-discretized mesh-less code (GIZMO). Using standard refinement criteria, we find that RAMSES produces a disc that is less vertically concentrated and does not reach such high densities as the SPHNG or GIZMO runs. The gas surface density in the spiral arms increases at a lower rate for the RAMSES simulations compared to the other codes. There is also a greater degree of substructure in the SPHNG and GIZMO runs and secondary spiral arms are more pronounced. By resolving the Jeans length with a greater number of grid cells, we achieve more similar results to the Lagrangian codes used in this study. Other alterations to the refinement scheme (adding extra levels of refinement and refining based on local density gradients) are less successful in reducing the disparity between RAMSES and SPHNG/GIZMO. Although more similar, SPHNG displays different density distributions and vertical mass profiles to all modes of GIZMO (including the smoothed particle hydrodynamics version). This suggests differences also arise which are not intrinsic to the particular method but rather due to its implementation. The discrepancies between codes (in particular, the densities reached in the spiral arms) could potentially result in differences in the locations and time-scales for gravitational collapse, and therefore impact star formation activity in more complex galaxy disc simulations.

Smooth particle hydrodynamics: theory and application to the origin of the moon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Benz, W.

1986-01-01

The origin of the moon is modeled by the so-called smooth particle hydrodynamics (SPH) method (Lucy, 1977, Monaghan 1985) which substitutes to the fluid a finite set of extended particles, the hydrodynamics equations reduce to the equation of motion of individual particles. These equations of motion differ only from the standard gravitational N-body problem insofar that pressure gradients and viscosity terms have to be added to the gradient of the potential to derive the forces between the particles. The numerical tools developed for ''classical'' N-body problems can therefore be readily applied to solve 3 dimensional hydroynamical problems. 12 refs., 1more » fig.« less

Hydrodynamic simulations of microjetting from shock-loaded grooves

NASA Astrophysics Data System (ADS)

Roland, C.; de Rességuier, T.; Sollier, A.; Lescoute, E.; Soulard, L.; Loison, D.

2017-01-01

The interaction of a shock wave with a free surface which has geometrical defects, such as cavities or grooves, may lead to the ejection of micrometric debris at velocities of km/s. This process can be involved in many applications, like pyrotechnics or industrial safety. Recent laser shock experiments reported elsewhere in this conference have provided some insight into jet formation as well as jet tip velocities for various groove angles and shock pressures. Here, we present hydrodynamic simulations of these experiments, in both 2D and 3D geometries, using both finite element method and smoothed particle hydrodynamics. Numerical results are compared to several theoretical predictions including the Richtmyer-Meshkov instabilities. The role of the elastic-plastic behavior on jet formation is illustrated. Finally, the possibility to simulate the late stage of jet expansion and fragmentation is explored, to evaluate the mass distribution of the ejecta and their ballistic properties, still essentially unknown in the experiments.

Efficient radiative transfer techniques in hydrodynamic simulations

NASA Astrophysics Data System (ADS)

Mercer, A.; Stamatellos, D.; Dunhill, A.

2018-05-01

Radiative transfer is an important component of hydrodynamic simulations as it determines the thermal properties of a physical system. It is especially important in cases where heating and cooling regulate significant processes, such as in the collapse of molecular clouds, the development of gravitational instabilities in protostellar discs, disc-planet interactions, and planet migration. We compare two approximate radiative transfer methods which indirectly estimate optical depths within hydrodynamic simulations using two different metrics: (i) the gravitational potential and density of the gas (Stamatellos et al.), and (ii) the pressure scale-height (Lombardi et al.). We find that both methods are accurate for spherical configurations e.g. in collapsing molecular clouds and within clumps that form in protostellar discs. However, the pressure scale-height approach is more accurate in protostellar discs (low and high-mass discs, discs with spiral features, discs with embedded planets). We also investigate the β-cooling approximation which is commonly used when simulating protostellar discs, and in which the cooling time is proportional to the orbital period of the gas. We demonstrate that the use of a constant β cannot capture the wide range of spatial and temporal variations of cooling in protostellar discs, which may affect the development of gravitational instabilities, planet migration, planet mass growth, and the orbital properties of planets.

3D Radiative Transfer in Eta Carinae: Application of the SimpleX Algorithm to 3D SPH Simulations of Binary Colliding Winds

NASA Technical Reports Server (NTRS)

Clementel, N.; Madura, T. I.; Kruip, C. J. H.; Icke, V.; Gull, T. R.

2014-01-01

Eta Carinae is an ideal astrophysical laboratory for studying massive binary interactions and evolution, and stellar wind-wind collisions. Recent three-dimensional (3D) simulations set the stage for understanding the highly complex 3D flows in Eta Car. Observations of different broad high- and low-ionization forbidden emission lines provide an excellent tool to constrain the orientation of the system, the primary's mass-loss rate, and the ionizing flux of the hot secondary. In this work we present the first steps towards generating synthetic observations to compare with available and future HST/STIS data. We present initial results from full 3D radiative transfer simulations of the interacting winds in Eta Car. We use the SimpleX algorithm to post-process the output from 3D SPH simulations and obtain the ionization fractions of hydrogen and helium assuming three different mass-loss rates for the primary star. The resultant ionization maps of both species constrain the regions where the observed forbidden emission lines can form. Including collisional ionization is necessary to achieve a better description of the ionization states, especially in the areas shielded from the secondary's radiation. We find that reducing the primary's mass-loss rate increases the volume of ionized gas, creating larger areas where the forbidden emission lines can form. We conclude that post processing 3D SPH data with SimpleX is a viable tool to create ionization maps for Eta Car.

3D Radiative Transfer in Eta Carinae: Application of the SimpleX Algorithm to 3D SPH Simulations of Binary Colliding Winds

NASA Technical Reports Server (NTRS)

Clementel, N.; Madura, T. I.; Kruip, C.J.H.; Icke, V.; Gull, T. R.

2014-01-01

Eta Carinae is an ideal astrophysical laboratory for studying massive binary interactions and evolution, and stellar wind-wind collisions. Recent three-dimensional (3D) simulations set the stage for understanding the highly complex 3D flows in eta Car. Observations of different broad high- and low-ionization forbidden emission lines provide an excellent tool to constrain the orientation of the system, the primary's mass-loss rate, and the ionizing flux of the hot secondary. In this work we present the first steps towards generating synthetic observations to compare with available and future HST/STIS data. We present initial results from full 3D radiative transfer simulations of the interacting winds in eta Car.We use the SimpleX algorithm to post-process the output from 3D SPH simulations and obtain the ionization fractions of hydrogen and helium assuming three different mass-loss rates for the primary star. The resultant ionization maps of both species constrain the regions where the observed forbidden emission lines can form. Including collisional ionization is necessary to achieve a better description of the ionization states, especially in the areas shielded from the secondary's radiation. We find that reducing the primary's mass-loss rate increases the volume of ionized gas, creating larger areas where the forbidden emission lines can form.We conclude that post processing 3D SPH data with SimpleX is a viable tool to create ionization maps for eta Car.

Can numerical simulations accurately predict hydrodynamic instabilities in liquid films?

NASA Astrophysics Data System (ADS)

Denner, Fabian; Charogiannis, Alexandros; Pradas, Marc; van Wachem, Berend G. M.; Markides, Christos N.; Kalliadasis, Serafim

2014-11-01

Understanding the dynamics of hydrodynamic instabilities in liquid film flows is an active field of research in fluid dynamics and non-linear science in general. Numerical simulations offer a powerful tool to study hydrodynamic instabilities in film flows and can provide deep insights into the underlying physical phenomena. However, the direct comparison of numerical results and experimental results is often hampered by several reasons. For instance, in numerical simulations the interface representation is problematic and the governing equations and boundary conditions may be oversimplified, whereas in experiments it is often difficult to extract accurate information on the fluid and its behavior, e.g. determine the fluid properties when the liquid contains particles for PIV measurements. In this contribution we present the latest results of our on-going, extensive study on hydrodynamic instabilities in liquid film flows, which includes direct numerical simulations, low-dimensional modelling as well as experiments. The major focus is on wave regimes, wave height and wave celerity as a function of Reynolds number and forcing frequency of a falling liquid film. Specific attention is paid to the differences in numerical and experimental results and the reasons for these differences. The authors are grateful to the EPSRC for their financial support (Grant EP/K008595/1).

Kinetically controlled synthesis of Au102(SPh)44 nanoclusters and catalytic application

NASA Astrophysics Data System (ADS)

Chen, Yongdong; Wang, Jin; Liu, Chao; Li, Zhimin; Li, Gao

2016-05-01

We here explore a kinetically controlled synthetic protocol for preparing solvent-solvable Au102(SPh)44 nanoclusters which are isolated from polydispersed gold nanoclusters by solvent extraction and size exclusion chromatography (SEC). The as-obtained Au102(SPh)44 nanoclusters are determined by matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) mass spectrometry, in conjunction with UV-vis spectroscopy and thermogravimetric analysis (TGA). However, Au99(SPh)42, instead of Au102(SPh)44, is yielded when the polydispersed gold nanoclusters are etched in the presence of excess thiophenol under thermal conditions (e.g., 80 °C). Interestingly, the Au102(SPh)44 nanoclusters also can convert to Au99(SPh)42 with equivalent thiophenol ligands, evidenced by the analyses of UV-vis and MALDI mass spectrometry. Finally, the TiO2-supported Au102(SPh)44 nanocluster catalyst is investigated in the selective oxidation of sulfides into sulfoxides by the PhIO oxidant and gives rise to high catalytic activity (e.g., 80-99% conversion of R-S-R' sulfides with 96-99% selectivity for R-S(&z.dbd;O)-R' sulfoxides). The Au102(SPh)44/TiO2 catalyst also shows excellent recyclability in the sulfoxidation process.We here explore a kinetically controlled synthetic protocol for preparing solvent-solvable Au102(SPh)44 nanoclusters which are isolated from polydispersed gold nanoclusters by solvent extraction and size exclusion chromatography (SEC). The as-obtained Au102(SPh)44 nanoclusters are determined by matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) mass spectrometry, in conjunction with UV-vis spectroscopy and thermogravimetric analysis (TGA). However, Au99(SPh)42, instead of Au102(SPh)44, is yielded when the polydispersed gold nanoclusters are etched in the presence of excess thiophenol under thermal conditions (e.g., 80 °C). Interestingly, the Au102(SPh)44 nanoclusters also can convert to Au99(SPh)42 with equivalent

Characterization of a serine proteinase homologous (SPH) in Chinese mitten crab Eriocheir sinensis.

PubMed

Qin, Chuanjie; Chen, Liqiao; Qin, Jian G; Zhao, Daxian; Zhang, Hao; Wu, Ping; Li, Erchao

2010-01-01

The serine protease homologous (SPH) is an important cofactor of prophenoloxidase-activating enzyme (PPAE). The gene of SPH of Chinese mitten crab Eriocheir sinensis (EsSPH) in hemocytes was cloned and characterized using reverse transcript polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE). The SPH cDNA consisted of 1386 bp with an open reading frame (ORF) encoded a protein of 378 amino acids, 154 bp 5'-untranslated region, and 95 bp 3'-untranslated region. Sequence comparisons against the GenBank database showed that EsSPH deduced amino acids had an overall identity to the gene of serine protease family from 41% to 70% of 15 invertebrate species. The protein had the structural characteristics of SPH, including the conserved six cysteine residues in the N-terminal clip domain and the functional activity (His157, Asp209, Gly311) in the C-terminal serine proteinase-like domain. To analyze the role of EsSPH in an acute infection, the temporal expression of the EsSPH gene after the Aeromonas hydrophila challenge was measured by real-time RT-PCR. The EsSPH transcripts in hemocytes significantly increased at 6 h, 12 h and 48 h over time after the A. hydrophila injection. This expression pattern shows that EsSPH has the potential to defend against invading microorganisms. The mRNA transcripts of EsSPH were detected in all tissues with the highest in the hepatopancreas. Interestingly, the mRNA transcripts of EsSPH and proPO were found in ova and expressed in oosperms, suggesting that the maternal transfer of EsSPH and proPO may exit in crab, but this warrants confirmation in further research.

General Relativistic Smoothed Particle Hydrodynamics code developments: A progress report

NASA Astrophysics Data System (ADS)

Faber, Joshua; Silberman, Zachary; Rizzo, Monica

2017-01-01

We report on our progress in developing a new general relativistic Smoothed Particle Hydrodynamics (SPH) code, which will be appropriate for studying the properties of accretion disks around black holes as well as compact object binary mergers and their ejecta. We will discuss in turn the relativistic formalisms being used to handle the evolution, our techniques for dealing with conservative and primitive variables, as well as those used to ensure proper conservation of various physical quantities. Code tests and performance metrics will be discussed, as will the prospects for including smoothed particle hydrodynamics codes within other numerical relativity codebases, particularly the publicly available Einstein Toolkit. We acknowledge support from NSF award ACI-1550436 and an internal RIT D-RIG grant.

Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations

PubMed Central

Ando, Tadashi; Chow, Edmond; Saad, Yousef; Skolnick, Jeffrey

2012-01-01

Hydrodynamic interactions play an important role in the dynamics of macromolecules. The most common way to take into account hydrodynamic effects in molecular simulations is in the context of a Brownian dynamics simulation. However, the calculation of correlated Brownian noise vectors in these simulations is computationally very demanding and alternative methods are desirable. This paper studies methods based on Krylov subspaces for computing Brownian noise vectors. These methods are related to Chebyshev polynomial approximations, but do not require eigenvalue estimates. We show that only low accuracy is required in the Brownian noise vectors to accurately compute values of dynamic and static properties of polymer and monodisperse suspension models. With this level of accuracy, the computational time of Krylov subspace methods scales very nearly as O(N2) for the number of particles N up to 10 000, which was the limit tested. The performance of the Krylov subspace methods, especially the “block” version, is slightly better than that of the Chebyshev method, even without taking into account the additional cost of eigenvalue estimates required by the latter. Furthermore, at N = 10 000, the Krylov subspace method is 13 times faster than the exact Cholesky method. Thus, Krylov subspace methods are recommended for performing large-scale Brownian dynamics simulations with hydrodynamic interactions. PMID:22897254

Self-perception of health (SPH) in the oldest-old subjects.

PubMed

Zikic, L; Jankelic, S; Milosevic, D P; Despotovic, N; Erceg, P; Davidovic, M

2009-01-01

SPH is a subjective and objective assessment of personal health. It is important in evaluation of health status in the elderly as it has capacity to predict mortality, functional declining, and health-care demands. A lot of research has been published about SPH in the elderly, but little is known about SPH in the very old, especially in comparison with the "younger-old" (YO) population. The study has aimed to investigate SPH in 240 elderly patients and compare the data between the "oldest-old" (OO) (aged >or= 90 years; n=52) and the YO (aged 60-74 years; n=188) subjects. Results have shown that the OO group of patients had better SPH than their YO counterparts. Our findings implicate that very old persons belong to a special sub-group of elderly, the "successfully aged", probably due to their genetic stability, distinctive lifestyle, or both.

Implementation of the SPH Procedure Within the MOOSE Finite Element Framework

NASA Astrophysics Data System (ADS)

Laurier, Alexandre

The goal of this thesis was to implement the SPH homogenization procedure within the MOOSE finite element framework at INL. Before this project, INL relied on DRAGON to do their SPH homogenization which was not flexible enough for their needs. As such, the SPH procedure was implemented for the neutron diffusion equation with the traditional, Selengut and true Selengut normalizations. Another aspect of this research was to derive the SPH corrected neutron transport equations and implement them in the same framework. Following in the footsteps of other articles, this feature was implemented and tested successfully with both the PN and S N transport calculation schemes. Although the results obtained for the power distribution in PWR assemblies show no advantages over the use of the SPH diffusion equation, we believe the inclusion of this transport correction will allow for better results in cases where either P N or SN are required. An additional aspect of this research was the implementation of a novel way of solving the non-linear SPH problem. Traditionally, this was done through a Picard, fixed-point iterative process whereas the new implementation relies on MOOSE's Preconditioned Jacobian-Free Newton Krylov (PJFNK) method to allow for a direct solution to the non-linear problem. This novel implementation showed a decrease in calculation time by a factor reaching 50 and generated SPH factors that correspond to those obtained through a fixed-point iterative process with a very tight convergence criteria: epsilon < 10-8. The use of the PJFNK SPH procedure also allows to reach convergence in problems containing important reflector regions and void boundary conditions, something that the traditional SPH method has never been able to achieve. At times when the PJFNK method cannot reach convergence to the SPH problem, a hybrid method is used where by the traditional SPH iteration forces the initial condition to be within the radius of convergence of the Newton method

Au38(SPh)24: Au38 Protected with Aromatic Thiolate Ligands.

PubMed

Rambukwella, Milan; Burrage, Shayna; Neubrander, Marie; Baseggio, Oscar; Aprà, Edoardo; Stener, Mauro; Fortunelli, Alessandro; Dass, Amala

2017-04-06

Au 38 (SR) 24 is one of the most extensively investigated gold nanomolecules along with Au 25 (SR) 18 and Au 144 (SR) 60 . However, so far it has only been prepared using aliphatic-like ligands, where R = -SC 6 H 13 , -SC 12 H 25 and -SCH 2 CH 2 Ph. Au 38 (SCH 2 CH 2 Ph) 24 when reacted with HSPh undergoes core-size conversion to Au 36 (SPh) 24 , and existing literature suggests that Au 38 (SPh) 24 cannot be synthesized. Here, contrary to prevailing knowledge, we demonstrate that Au 38 (SPh) 24 can be prepared if the ligand exchanged conditions are optimized, under delicate conditions, without any formation of Au 36 (SPh) 24 . Conclusive evidence is presented in the form of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), electrospray ionization mass spectra (ESI-MS) characterization, and optical spectra of Au 38 (SPh) 24 in a solid glass form showing distinct differences from that of Au 38 (S-aliphatic) 24 . Theoretical analysis confirms experimental assignment of the optical spectrum and shows that the stability of Au 38 (SPh) 24 is not negligible with respect to that of its aliphatic analogous, and contains a significant component of ligand-ligand attractive interactions. Thus, while Au 38 (SPh) 24 is stable at RT, it converts to Au 36 (SPh) 24 either on prolonged etching (longer than 2 hours) at RT or when etched at 80 °C.

Classifying and modelling spiral structures in hydrodynamic simulations of astrophysical discs

NASA Astrophysics Data System (ADS)

Forgan, D. H.; Ramón-Fox, F. G.; Bonnell, I. A.

2018-05-01

We demonstrate numerical techniques for automatic identification of individual spiral arms in hydrodynamic simulations of astrophysical discs. Building on our earlier work, which used tensor classification to identify regions that were `spiral-like', we can now obtain fits to spirals for individual arm elements. We show this process can even detect spirals in relatively flocculent spiral patterns, but the resulting fits to logarithmic `grand-design' spirals are less robust. Our methods not only permit the estimation of pitch angles, but also direct measurements of the spiral arm width and pattern speed. In principle, our techniques will allow the tracking of material as it passes through an arm. Our demonstration uses smoothed particle hydrodynamics simulations, but we stress that the method is suitable for any finite-element hydrodynamics system. We anticipate our techniques will be essential to studies of star formation in disc galaxies, and attempts to find the origin of recently observed spiral structure in protostellar discs.

Gas stripping and mixing in galaxy clusters: a numerical comparison study

NASA Astrophysics Data System (ADS)

Heß, Steffen; Springel, Volker

2012-11-01

The ambient hot intrahalo gas in clusters of galaxies is constantly fed and stirred by infalling galaxies, a process that can be studied in detail with cosmological hydrodynamical simulations. However, different numerical methods yield discrepant predictions for crucial hydrodynamical processes, leading for example to different entropy profiles in clusters of galaxies. In particular, the widely used Lagrangian smoothed particle hydrodynamics (SPH) scheme is suspected to strongly damp fluid instabilities and turbulence, which are both crucial to establish the thermodynamic structure of clusters. In this study, we test to which extent our recently developed Voronoi particle hydrodynamics (VPH) scheme yields different results for the stripping of gas out of infalling galaxies and for the bulk gas properties of cluster. We consider both the evolution of isolated galaxy models that are exposed to a stream of intracluster medium or are dropped into cluster models, as well as non-radiative cosmological simulations of cluster formation. We also compare our particle-based method with results obtained with a fundamentally different discretization approach as implemented in the moving-mesh code AREPO. We find that VPH leads to noticeably faster stripping of gas out of galaxies than SPH, in better agreement with the mesh-code than with SPH. We show that despite the fact that VPH in its present form is not as accurate as the moving mesh code in our investigated cases, its improved accuracy of gradient estimates makes VPH an attractive alternative to SPH.

Kinetically controlled synthesis of Au102(SPh)44 nanoclusters and catalytic application.

PubMed

Chen, Yongdong; Wang, Jin; Liu, Chao; Li, Zhimin; Li, Gao

2016-05-21

We here explore a kinetically controlled synthetic protocol for preparing solvent-solvable Au102(SPh)44 nanoclusters which are isolated from polydispersed gold nanoclusters by solvent extraction and size exclusion chromatography (SEC). The as-obtained Au102(SPh)44 nanoclusters are determined by matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) mass spectrometry, in conjunction with UV-vis spectroscopy and thermogravimetric analysis (TGA). However, Au99(SPh)42, instead of Au102(SPh)44, is yielded when the polydispersed gold nanoclusters are etched in the presence of excess thiophenol under thermal conditions (e.g., 80 °C). Interestingly, the Au102(SPh)44 nanoclusters also can convert to Au99(SPh)42 with equivalent thiophenol ligands, evidenced by the analyses of UV-vis and MALDI mass spectrometry. Finally, the TiO2-supported Au102(SPh)44 nanocluster catalyst is investigated in the selective oxidation of sulfides into sulfoxides by the PhIO oxidant and gives rise to high catalytic activity (e.g., 80-99% conversion of R-S-R' sulfides with 96-99% selectivity for R-S([double bond, length as m-dash]O)-R' sulfoxides). The Au102(SPh)44/TiO2 catalyst also shows excellent recyclability in the sulfoxidation process.

Simulations of sheared dense noncolloidal suspensions: Evaluation of the role of long-range hydrodynamics

NASA Astrophysics Data System (ADS)

Gallier, Stany; Peters, François; Lobry, Laurent

2018-04-01

This work intends to evaluate the role of many-body long-range hydrodynamics by simulations of sheared neutrally buoyant non-Brownian, noncolloidal suspensions. Three-dimensional simulations of sheared suspensions are conducted with and without long-range hydrodynamics, for a volume fraction range between 0.1-0.62 (frictionless) and 0.1-0.56 (frictional). Discarding long-range hydrodynamics has only a moderate effect on viscosity for the range of volume fractions investigated and viscosities diverge with similar scaling laws; the critical fraction is found to be approximately 0.64 (frictionless) and 0.58 (frictional). Conversely, many-body hydrodynamics are found to affect diffusion and particle velocities, which are correlated on a longer range when long-range interactions are included, even in dense suspensions. This means that long-range hydrodynamics may not be significantly screened by crowding. Assuming only short-range lubrication interactions is therefore suitable for predicting viscosity in noncolloidal suspensions but becomes questionable when flow details (e.g., diffusion or velocity correlations) are needed.

The Formation of a Milky Way-sized Disk Galaxy. I. A Comparison of Numerical Methods

NASA Astrophysics Data System (ADS)

Zhu, Qirong; Li, Yuexing

2016-11-01

The long-standing challenge of creating a Milky Way- (MW-) like disk galaxy from cosmological simulations has motivated significant developments in both numerical methods and physical models. We investigate these two fundamental aspects in a new comparison project using a set of cosmological hydrodynamic simulations of an MW-sized galaxy. In this study, we focus on the comparison of two particle-based hydrodynamics methods: an improved smoothed particle hydrodynamics (SPH) code Gadget, and a Lagrangian Meshless Finite-Mass (MFM) code Gizmo. All the simulations in this paper use the same initial conditions and physical models, which include star formation, “energy-driven” outflows, metal-dependent cooling, stellar evolution, and metal enrichment. We find that both numerical schemes produce a late-type galaxy with extended gaseous and stellar disks. However, notable differences are present in a wide range of galaxy properties and their evolution, including star-formation history, gas content, disk structure, and kinematics. Compared to Gizmo, the Gadget simulation produced a larger fraction of cold, dense gas at high redshift which fuels rapid star formation and results in a higher stellar mass by 20% and a lower gas fraction by 10% at z = 0, and the resulting gas disk is smoother and more coherent in rotation due to damping of turbulent motion by the numerical viscosity in SPH, in contrast to the Gizmo simulation, which shows a more prominent spiral structure. Given its better convergence properties and lower computational cost, we argue that the MFM method is a promising alternative to SPH in cosmological hydrodynamic simulations.

THE FORMATION OF A MILKY WAY-SIZED DISK GALAXY. I. A COMPARISON OF NUMERICAL METHODS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Qirong; Li, Yuexing, E-mail: qxz125@psu.edu

The long-standing challenge of creating a Milky Way- (MW-) like disk galaxy from cosmological simulations has motivated significant developments in both numerical methods and physical models. We investigate these two fundamental aspects in a new comparison project using a set of cosmological hydrodynamic simulations of an MW-sized galaxy. In this study, we focus on the comparison of two particle-based hydrodynamics methods: an improved smoothed particle hydrodynamics (SPH) code Gadget, and a Lagrangian Meshless Finite-Mass (MFM) code Gizmo. All the simulations in this paper use the same initial conditions and physical models, which include star formation, “energy-driven” outflows, metal-dependent cooling, stellarmore » evolution, and metal enrichment. We find that both numerical schemes produce a late-type galaxy with extended gaseous and stellar disks. However, notable differences are present in a wide range of galaxy properties and their evolution, including star-formation history, gas content, disk structure, and kinematics. Compared to Gizmo, the Gadget simulation produced a larger fraction of cold, dense gas at high redshift which fuels rapid star formation and results in a higher stellar mass by 20% and a lower gas fraction by 10% at z = 0, and the resulting gas disk is smoother and more coherent in rotation due to damping of turbulent motion by the numerical viscosity in SPH, in contrast to the Gizmo simulation, which shows a more prominent spiral structure. Given its better convergence properties and lower computational cost, we argue that the MFM method is a promising alternative to SPH in cosmological hydrodynamic simulations.« less

Dynamic simulation of concentrated macromolecular solutions with screened long-range hydrodynamic interactions: Algorithm and limitations

PubMed Central

Ando, Tadashi; Chow, Edmond; Skolnick, Jeffrey

2013-01-01

Hydrodynamic interactions exert a critical effect on the dynamics of macromolecules. As the concentration of macromolecules increases, by analogy to the behavior of semidilute polymer solutions or the flow in porous media, one might expect hydrodynamic screening to occur. Hydrodynamic screening would have implications both for the understanding of macromolecular dynamics as well as practical implications for the simulation of concentrated macromolecular solutions, e.g., in cells. Stokesian dynamics (SD) is one of the most accurate methods for simulating the motions of N particles suspended in a viscous fluid at low Reynolds number, in that it considers both far-field and near-field hydrodynamic interactions. This algorithm traditionally involves an O(N3) operation to compute Brownian forces at each time step, although asymptotically faster but more complex SD methods are now available. Motivated by the idea of hydrodynamic screening, the far-field part of the hydrodynamic matrix in SD may be approximated by a diagonal matrix, which is equivalent to assuming that long range hydrodynamic interactions are completely screened. This approximation allows sparse matrix methods to be used, which can reduce the apparent computational scaling to O(N). Previously there were several simulation studies using this approximation for monodisperse suspensions. Here, we employ newly designed preconditioned iterative methods for both the computation of Brownian forces and the solution of linear systems, and consider the validity of this approximation in polydisperse suspensions. We evaluate the accuracy of the diagonal approximation method using an intracellular-like suspension. The diffusivities of particles obtained with this approximation are close to those with the original method. However, this approximation underestimates intermolecular correlated motions, which is a trade-off between accuracy and computing efficiency. The new method makes it possible to perform large-scale and

Three-dimensional hydrodynamic simulations of OMEGA implosions

NASA Astrophysics Data System (ADS)

Igumenshchev, I. V.; Michel, D. T.; Shah, R. C.; Campbell, E. M.; Epstein, R.; Forrest, C. J.; Glebov, V. Yu.; Goncharov, V. N.; Knauer, J. P.; Marshall, F. J.; McCrory, R. L.; Regan, S. P.; Sangster, T. C.; Stoeckl, C.; Schmitt, A. J.; Obenschain, S.

2017-05-01

The effects of large-scale (with Legendre modes ≲ 10) asymmetries in OMEGA direct-drive implosions caused by laser illumination nonuniformities (beam-power imbalance and beam mispointing and mistiming), target offset, and variation in target-layer thickness were investigated using the low-noise, three-dimensional Eulerian hydrodynamic code ASTER. Simulations indicate that these asymmetries can significantly degrade the implosion performance. The most important sources of the asymmetries are the target offsets ( ˜10 to 20 μm), beam-power imbalance ( σrms˜10 %), and variations ( ˜5 %) in target-layer thickness. Large-scale asymmetries distort implosion cores, resulting in a reduced hot-spot confinement and an increased residual kinetic energy of implosion targets. The ion temperature inferred from the width of simulated neutron spectra is influenced by bulk fuel motion in the distorted hot spot and can result in up to an ˜1 -keV increase in apparent temperature. Similar temperature variations along different lines of sight are observed. Demonstrating hydrodynamic equivalence to ignition designs on OMEGA requires a reduction in large-scale target and laser-imposed nonuniformities, minimizing target offset, and employing highly efficient mid-adiabat (α = 4) implosion designs, which mitigate cross-beam energy transfer and suppress short-wavelength Rayleigh-Taylor growth.

Three-dimensional hydrodynamic simulations of OMEGA implosions

DOE PAGES

Igumenshchev, I. V.; Michel, D. T.; Shah, R. C.; ...

2017-03-30

Here, the effects of large-scale (with Legendre modes ≲10) asymmetries in OMEGA direct-drive implosions caused by laser illumination nonuniformities (beam-power imbalance and beam mispointing and mistiming), target offset, and variation in target-layer thickness were investigated using the low-noise, three-dimensional Eulerian hydrodynamic code ASTER. Simulations indicate that these asymmetries can significantly degrade the implosion performance. The most important sources of the asymmetries are the target offsets (~10 to 20 μm), beam-power imbalance (σ rms ~ 10%), and variations (~5%) in target-layer thickness. Large-scale asymmetries distort implosion cores, resulting in a reduced hot-spot confinement and an increased residual kinetic energy of implosionmore » targets. The ion temperature inferred from the width of simulated neutron spectra is influenced by bulk fuel motion in the distorted hot spot and can result in up to an ~1 -keV increase in apparent temperature. Similar temperature variations along different lines of sight are observed. Demonstrating hydrodynamic equivalence to ignition designs on OMEGA requires a reduction in large-scale target and laser-imposed nonuniformities, minimizing target offset, and employing highly efficient mid-adiabat (α = 4) implosion designs, which mitigate cross-beam energy transfer and suppress short-wavelength Rayleigh–Taylor growth.« less

Three-dimensional hydrodynamic simulations of OMEGA implosions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Igumenshchev, I. V.; Michel, D. T.; Shah, R. C.

Here, the effects of large-scale (with Legendre modes ≲10) asymmetries in OMEGA direct-drive implosions caused by laser illumination nonuniformities (beam-power imbalance and beam mispointing and mistiming), target offset, and variation in target-layer thickness were investigated using the low-noise, three-dimensional Eulerian hydrodynamic code ASTER. Simulations indicate that these asymmetries can significantly degrade the implosion performance. The most important sources of the asymmetries are the target offsets (~10 to 20 μm), beam-power imbalance (σ rms ~ 10%), and variations (~5%) in target-layer thickness. Large-scale asymmetries distort implosion cores, resulting in a reduced hot-spot confinement and an increased residual kinetic energy of implosionmore » targets. The ion temperature inferred from the width of simulated neutron spectra is influenced by bulk fuel motion in the distorted hot spot and can result in up to an ~1 -keV increase in apparent temperature. Similar temperature variations along different lines of sight are observed. Demonstrating hydrodynamic equivalence to ignition designs on OMEGA requires a reduction in large-scale target and laser-imposed nonuniformities, minimizing target offset, and employing highly efficient mid-adiabat (α = 4) implosion designs, which mitigate cross-beam energy transfer and suppress short-wavelength Rayleigh–Taylor growth.« less

SPH simulations of WBC adhesion to the endothelium: the role of haemodynamics and endothelial binding kinetics.

PubMed

Gholami, Babak; Comerford, Andrew; Ellero, Marco

2015-11-01

A multiscale Lagrangian particle solver introduced in our previous work is extended to model physiologically realistic near-wall cell dynamics. Three-dimensional simulation of particle trajectories is combined with realistic receptor-ligand adhesion behaviour to cover full cell interactions in the vicinity of the endothelium. The selected stochastic adhesion model, which is based on a Monte Carlo acceptance-rejection method, fits in our Lagrangian framework and does not compromise performance. Additionally, appropriate inflow/outflow boundary conditions are implemented for our SPH solver to enable realistic pulsatile flow simulation. The model is tested against in-vitro data from a 3D geometry with a stenosis and sudden expansion. In both steady and pulsatile flow conditions, results show close agreement with the experimental ones. Furthermore we demonstrate, in agreement with experimental observations, that haemodynamics alone does not account for adhesion of white blood cells, in this case U937 monocytic human cells. Our findings suggest that the current framework is fully capable of modelling cell dynamics in large arteries in a realistic and efficient manner.

A simple way to improve AGN feedback prescription in SPH simulations

NASA Astrophysics Data System (ADS)

Zubovas, Kastytis; Bourne, Martin A.; Nayakshin, Sergei

2016-03-01

Active galactic nuclei (AGN) feedback is an important ingredient in galaxy evolution, however its treatment in numerical simulations is necessarily approximate, requiring subgrid prescriptions due to the dynamical range involved in the calculations. We present a suite of smoothed particle hydrodynamics simulations designed to showcase the importance of the choice of a particular subgrid prescription for AGN feedback. We concentrate on two approaches to treating wide-angle AGN outflows: thermal feedback, where thermal and kinetic energy is injected into the gas surrounding the supermassive black hole (SMBH) particle, and virtual particle feedback, where energy is carried by tracer particles radially away from the AGN. We show that the latter model produces a far more complex structure around the SMBH, which we argue is a more physically correct outcome. We suggest a simple improvement to the thermal feedback model - injecting the energy into a cone, rather than spherically symmetrically - and show that this markedly improves the agreement between the two prescriptions, without requiring any noticeable increase in the computational cost of the simulation.

Cosmological Hydrodynamics on a Moving Mesh

NASA Astrophysics Data System (ADS)

Hernquist, Lars

We propose to construct a model for the visible Universe using cosmological simulations of structure formation. Our simulations will include both dark matter and baryons, and will employ two entirely different schemes for evolving the gas: smoothed particle hydrodynamics (SPH) and a moving mesh approach as incorporated in the new code, AREPO. By performing simulations that are otherwise nearly identical, except for the hydrodynamics solver, we will isolate and understand differences in the properties of galaxies, galaxy groups and clusters, and the intergalactic medium caused by the computational approach that have plagued efforts to understand galaxy formation for nearly two decades. By performing simulations at different levels of resolution and with increasingly complex treatments of the gas physics, we will identify the results that are converged numerically and that are robust with respect to variations in unresolved physical processes, especially those related to star formation, black hole growth, and related feedback effects. In this manner, we aim to undertake a research program that will redefine the state of the art in cosmological hydrodynamics and galaxy formation. In particular, we will focus our scientific efforts on understanding: 1) the formation of galactic disks in a cosmological context; 2) the physical state of diffuse gas in galaxy clusters and groups so that they can be used as high-precision probes of cosmology; 3) the nature of gas inflows into galaxy halos and the subsequent accretion of gas by forming disks; 4) the co-evolution of galaxies and galaxy clusters with their central supermassive black holes and the implications of related feedback for galaxy evolution and the dichotomy between blue and red galaxies; 5) the physical state of the intergalactic medium (IGM) and the evolution of the metallicity of the IGM; and 6) the reaction of dark matter around galaxies to galaxy formation. Our proposed work will be of immediate significance for

Hydrodynamic instabilities at an oblique interface: Experiments and Simulations

NASA Astrophysics Data System (ADS)

Douglas-Mann, E.; Fiedler Kawaguchi, C.; Trantham, M. A.; Malamud, G.; Wan, W. C.; Klein, S. R.; Kuranz, C. C.

2017-10-01

Hydrodynamic instabilities are important phenomena that occur in high-energy-density systems, such as astrophysical systems and inertial confinement fusion experiments, where pressure, density, and velocity gradients are present. Using a 30 ns laser pulse from the Omega EP laser system, a steady shock wave is driven into a target. A Spherical Crystal Imager provides high-resolution x-ray radiographs to study the evolution of complex hydrodynamic structures. This experiment has a light-to-heavy interface at an oblique angle with a precision-machined perturbation. The incident shock wave deposits shear and vorticity at the interface causing the perturbation to grow via Richtmyer-Meshkov and Kelvin-Helmholtz processes. We present results from analysis of radiographic data and hydrodynamics simulations showing the evolution of the shock and unstable structure. This work is supported by the NNSA-DS and SC-OFES Joint Program in High-Energy-Density Laboratory Plasmas, Grant Number DE-NA0002956 and the National Science Foundation through the Basic Plasma Science and Engineering program and LILAC.

A hybrid method for flood simulation in small catchments combining hydrodynamic and hydrological techniques

NASA Astrophysics Data System (ADS)

Bellos, Vasilis; Tsakiris, George

2016-09-01

The study presents a new hybrid method for the simulation of flood events in small catchments. It combines a physically-based two-dimensional hydrodynamic model and the hydrological unit hydrograph theory. Unit hydrographs are derived using the FLOW-R2D model which is based on the full form of two-dimensional Shallow Water Equations, solved by a modified McCormack numerical scheme. The method is tested at a small catchment in a suburb of Athens-Greece for a storm event which occurred in February 2013. The catchment is divided into three friction zones and unit hydrographs of 15 and 30 min are produced. The infiltration process is simulated by the empirical Kostiakov equation and the Green-Ampt model. The results from the implementation of the proposed hybrid method are compared with recorded data at the hydrometric station at the outlet of the catchment and the results derived from the fully hydrodynamic model FLOW-R2D. It is concluded that for the case studied, the proposed hybrid method produces results close to those of the fully hydrodynamic simulation at substantially shorter computational time. This finding, if further verified in a variety of case studies, can be useful in devising effective hybrid tools for the two-dimensional flood simulations, which are lead to accurate and considerably faster results than those achieved by the fully hydrodynamic simulations.

FLASH hydrodynamic simulations of experiments to explore the generation of cosmological magnetic fields

NASA Astrophysics Data System (ADS)

Scopatz, A.; Fatenejad, M.; Flocke, N.; Gregori, G.; Koenig, M.; Lamb, D. Q.; Lee, D.; Meinecke, J.; Ravasio, A.; Tzeferacos, P.; Weide, K.; Yurchak, R.

2013-03-01

We report the results of FLASH hydrodynamic simulations of the experiments conducted by the University of Oxford High Energy Density Laboratory Astrophysics group and its collaborators at the Laboratoire pour l'Utilisation de Lasers Intenses (LULI). In these experiments, a long-pulse laser illuminates a target in a chamber filled with Argon gas, producing shock waves that generate magnetic fields via the Biermann battery mechanism. The simulations show that the result of the laser illuminating the target is a series of complex hydrodynamic phenomena.

Galaxy-halo alignments in the Horizon-AGN cosmological hydrodynamical simulation

NASA Astrophysics Data System (ADS)

Chisari, N. E.; Koukoufilippas, N.; Jindal, A.; Peirani, S.; Beckmann, R. S.; Codis, S.; Devriendt, J.; Miller, L.; Dubois, Y.; Laigle, C.; Slyz, A.; Pichon, C.

2017-11-01

Intrinsic alignments of galaxies are a significant astrophysical systematic affecting cosmological constraints from weak gravitational lensing. Obtaining numerical predictions from hydrodynamical simulations of expected survey volumes is expensive, and a cheaper alternative relies on populating large dark matter-only simulations with accurate models of alignments calibrated on smaller hydrodynamical runs. This requires connecting the shapes and orientations of galaxies to those of dark matter haloes and to the large-scale structure. In this paper, we characterize galaxy-halo alignments in the Horizon-AGN cosmological hydrodynamical simulation. We compare the shapes and orientations of galaxies in the redshift range of 0 < z < 3 to those of their embedding dark matter haloes, and to the matching haloes of a twin dark-matter only run with identical initial conditions. We find that galaxy ellipticities, in general, cannot be predicted directly from halo ellipticities. The mean misalignment angle between the minor axis of a galaxy and its embedding halo is a function of halo mass, with residuals arising from the dependence of alignment on galaxy type, but not on environment. Haloes are much more strongly aligned among themselves than galaxies, and they decrease their alignment towards low redshift. Galaxy alignments compete with this effect, as galaxies tend to increase their alignment with haloes towards low redshift. We discuss the implications of these results for current halo models of intrinsic alignments and suggest several avenues for improvement.

A particle-based model to simulate the micromechanics of single-plant parenchyma cells and aggregates

NASA Astrophysics Data System (ADS)

Van Liedekerke, P.; Ghysels, P.; Tijskens, E.; Samaey, G.; Smeedts, B.; Roose, D.; Ramon, H.

2010-06-01

This paper is concerned with addressing how plant tissue mechanics is related to the micromechanics of cells. To this end, we propose a mesh-free particle method to simulate the mechanics of both individual plant cells (parenchyma) and cell aggregates in response to external stresses. The model considers two important features in the plant cell: (1) the cell protoplasm, the interior liquid phase inducing hydrodynamic phenomena, and (2) the cell wall material, a viscoelastic solid material that contains the protoplasm. In this particle framework, the cell fluid is modeled by smoothed particle hydrodynamics (SPH), a mesh-free method typically used to address problems with gas and fluid dynamics. In the solid phase (cell wall) on the other hand, the particles are connected by pairwise interactions holding them together and preventing the fluid to penetrate the cell wall. The cell wall hydraulic conductivity (permeability) is built in as well through the SPH formulation. Although this model is also meant to be able to deal with dynamic and even violent situations (leading to cell wall rupture or cell-cell debonding), we have concentrated on quasi-static conditions. The results of single-cell compression simulations show that the conclusions found by analytical models and experiments can be reproduced at least qualitatively. Relaxation tests revealed that plant cells have short relaxation times (1 µs-10 µs) compared to mammalian cells. Simulations performed on cell aggregates indicated an influence of the cellular organization to the tissue response, as was also observed in experiments done on tissues with a similar structure.

Smoothed Particle Hydrodynamics Continuous Boundary Force method for Navier-Stokes equations subject to Robin boundary condition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pan, Wenxiao; Bao, Jie; Tartakovsky, Alexandre M.

2014-02-15

Robin boundary condition for the Navier-Stokes equations is used to model slip conditions at the fluid-solid boundaries. A novel Continuous Boundary Force (CBF) method is proposed for solving the Navier-Stokes equations subject to Robin boundary condition. In the CBF method, the Robin boundary condition at boundary is replaced by the homogeneous Neumann boundary condition at the boundary and a volumetric force term added to the momentum conservation equation. Smoothed Particle Hydrodynamics (SPH) method is used to solve the resulting Navier-Stokes equations. We present solutions for two-dimensional and three-dimensional flows in domains bounded by flat and curved boundaries subject to variousmore » forms of the Robin boundary condition. The numerical accuracy and convergence are examined through comparison of the SPH-CBF results with the solutions of finite difference or finite element method. Taken the no-slip boundary condition as a special case of slip boundary condition, we demonstrate that the SPH-CBF method describes accurately both no-slip and slip conditions.« less

Implicit SPH v. 1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Kyungjoo; Parks, Michael L.; Perego, Mauro

2016-11-09

ISPH code is developed to solve multi-physics meso-scale flow problems using implicit SPH method. In particular, the code can provides solutions for incompressible, multi phase flow and electro-kinetic flows.

GENASIS: General Astrophysical Simulation System. I. Refinable Mesh and Nonrelativistic Hydrodynamics

NASA Astrophysics Data System (ADS)

Cardall, Christian Y.; Budiardja, Reuben D.; Endeve, Eirik; Mezzacappa, Anthony

2014-02-01

GenASiS (General Astrophysical Simulation System) is a new code being developed initially and primarily, though by no means exclusively, for the simulation of core-collapse supernovae on the world's leading capability supercomputers. This paper—the first in a series—demonstrates a centrally refined coordinate patch suitable for gravitational collapse and documents methods for compressible nonrelativistic hydrodynamics. We benchmark the hydrodynamics capabilities of GenASiS against many standard test problems; the results illustrate the basic competence of our implementation, demonstrate the strengths and limitations of the HLLC relative to the HLL Riemann solver in a number of interesting cases, and provide preliminary indications of the code's ability to scale and to function with cell-by-cell fixed-mesh refinement.

Theoretical and simulation research of hydrodynamic instabilities in inertial-confinement fusion implosions

NASA Astrophysics Data System (ADS)

Wang, LiFeng; Ye, WenHua; He, XianTu; Wu, JunFeng; Fan, ZhengFeng; Xue, Chuang; Guo, HongYu; Miao, WenYong; Yuan, YongTeng; Dong, JiaQin; Jia, Guo; Zhang, Jing; Li, YingJun; Liu, Jie; Wang, Min; Ding, YongKun; Zhang, WeiYan

2017-05-01

Inertial fusion energy (IFE) has been considered a promising, nearly inexhaustible source of sustainable carbon-free power for the world's energy future. It has long been recognized that the control of hydrodynamic instabilities is of critical importance for ignition and high-gain in the inertial-confinement fusion (ICF) hot-spot ignition scheme. In this mini-review, we summarize the progress of theoretical and simulation research of hydrodynamic instabilities in the ICF central hot-spot implosion in our group over the past decade. In order to obtain sufficient understanding of the growth of hydrodynamic instabilities in ICF, we first decompose the problem into different stages according to the implosion physics processes. The decomposed essential physics pro- cesses that are associated with ICF implosions, such as Rayleigh-Taylor instability (RTI), Richtmyer-Meshkov instability (RMI), Kelvin-Helmholtz instability (KHI), convergent geometry effects, as well as perturbation feed-through are reviewed. Analyti- cal models in planar, cylindrical, and spherical geometries have been established to study different physical aspects, including density-gradient, interface-coupling, geometry, and convergent effects. The influence of ablation in the presence of preheating on the RTI has been extensively studied by numerical simulations. The KHI considering the ablation effect has been discussed in detail for the first time. A series of single-mode ablative RTI experiments has been performed on the Shenguang-II laser facility. The theoretical and simulation research provides us the physical insights of linear and weakly nonlinear growths, and nonlinear evolutions of the hydrodynamic instabilities in ICF implosions, which has directly supported the research of ICF ignition target design. The ICF hot-spot ignition implosion design that uses several controlling features, based on our current understanding of hydrodynamic instabilities, to address shell implosion stability, has

nIFTY galaxy cluster simulations - III. The similarity and diversity of galaxies and subhaloes

NASA Astrophysics Data System (ADS)

Elahi, Pascal J.; Knebe, Alexander; Pearce, Frazer R.; Power, Chris; Yepes, Gustavo; Cui, Weiguang; Cunnama, Daniel; Kay, Scott T.; Sembolini, Federico; Beck, Alexander M.; Davé, Romeel; February, Sean; Huang, Shuiyao; Katz, Neal; McCarthy, Ian G.; Murante, Giuseppe; Perret, Valentin; Puchwein, Ewald; Saro, Alexandro; Teyssier, Romain

2016-05-01

We examine subhaloes and galaxies residing in a simulated Λ cold dark matter galaxy cluster (M^crit_{200}=1.1× 10^{15} h^{-1} M_{⊙}) produced by hydrodynamical codes ranging from classic smooth particle hydrodynamics (SPH), newer SPH codes, adaptive and moving mesh codes. These codes use subgrid models to capture galaxy formation physics. We compare how well these codes reproduce the same subhaloes/galaxies in gravity-only, non-radiative hydrodynamics and full feedback physics runs by looking at the overall subhalo/galaxy distribution and on an individual object basis. We find that the subhalo population is reproduced to within ≲10 per cent for both dark matter only and non-radiative runs, with individual objects showing code-to-code scatter of ≲0.1 dex, although the gas in non-radiative simulations shows significant scatter. Including feedback physics significantly increases the diversity. Subhalo mass and Vmax distributions vary by ≈20 per cent. The galaxy populations also show striking code-to-code variations. Although the Tully-Fisher relation is similar in almost all codes, the number of galaxies with 109 h- 1 M⊙ ≲ M* ≲ 1012 h- 1 M⊙ can differ by a factor of 4. Individual galaxies show code-to-code scatter of ˜0.5 dex in stellar mass. Moreover, systematic differences exist, with some codes producing galaxies 70 per cent smaller than others. The diversity partially arises from the inclusion/absence of active galactic nucleus feedback. Our results combined with our companion papers demonstrate that subgrid physics is not just subject to fine-tuning, but the complexity of building galaxies in all environments remains a challenge. We argue that even basic galaxy properties, such as stellar mass to halo mass, should be treated with errors bars of ˜0.2-0.4 dex.

Observing the baryon cycle in hydrodynamic cosmological simulations

NASA Astrophysics Data System (ADS)

Vander Vliet, Jacob Richard

An understanding of galaxy evolution requires an understanding of the flow of baryons in and out of a galaxy. The accretion of baryons is required for galaxies to form stars, while stars eject baryons out of the galaxy through stellar feedback mechanisms such as supernovae, stellar winds, and radiation pressure. The interplay between outfiowing and infalling material form the circumgalactic medium (CGM). Hydrodynamic simulations provide understanding of the connection between stellar feedback and the distribution and kinematics of baryons in the CGM. To compare simulations and observations properly the simulated CGI must be observed in the same manner as the real CGM. I have developed the Mockspec code to generate synthetic quasar absorption line observations of the CGM in cosmological hydrodynamic simulations. Mockspec generates synthetic spectra based on the phase; lnetallicity, and kinematics of CGM gas and mimics instrumental effects. Mockspec includes automated analysis of the spectra and identifies the gas responsible for the absorption. Mockspec was applied to simulations of dwarf galaxies at low redshift to examine the observable effect different feedback models have on the CGM. While the different feedback models had strong effects on the galaxy, they all produced a similar CGM that failed match observations. Mockspec was applied to the VELA simulation suite of high redshift, high mass galaxies to examine the variance of the CGM across different galaxies in different environments. The observed CGM showed little variation between the different galaxies and almost no evolution from z=4 to z=1. The VELAs were not able to generate a CGM to match the observations. The properties of cells responsible for the absorption were compared to the derived properties from Voigt Profile decomposition. VP modeling was found to accurately describe the HI and MgII absorbing gas but failed for high ionization species such as CIV and OVI, which do not arise in the coherent

RR Lyrae in the UMi dSph Galaxy

NASA Astrophysics Data System (ADS)

Kuehn, Charles; Kinemuchi, Karen; Jeffery, Elizabeth; Grabowski, Kathleen; Nemec, James; Herrera, Daniel

2018-01-01

Over the past two years we have obtained observations of the Ursa Minor dwarf spheroidal galaxy with the goal of completing an updated catalog of the variable stars in the dwarf galaxy. In addition to finding new variable stars, this updated catalog will allow us to look at period changes in the variables and to determine stellar characteristic for the RR Lyrae stars in the dSph. We will compare the RR Lyrae stellar characteristics to other RR Lyrae stars found in the Local Group dSph galaxies; these comparisons can give us insights to the near-field cosmology of the Local Group. In this poster we present our updated catalog of RR Lyrae stars in the UMi dSph; the updated catalog includes Fourier decomposition parameters, metallicities, and other physical properties for the RR Lyrae stars.

Overview of SPH-ALE applications for hydraulic turbines in ANDRITZ Hydro

NASA Astrophysics Data System (ADS)

Rentschler, M.; Marongiu, J. C.; Neuhauser, M.; Parkinson, E.

2018-02-01

Over the past 13 years, ANDRITZ Hydro has developed an in-house tool based on the SPH-ALE method for applications in flow simulations in hydraulic turbines. The initial motivation is related to the challenging simulation of free surface flows in Pelton turbines, where highly dynamic water jets interact with rotating buckets, creating thin water jets traveling inside the housing and possibly causing disturbances on the runner. The present paper proposes an overview of industrial applications allowed by the developed tool, including design evaluation of Pelton runners and casings, transient operation of Pelton units and free surface flows in hydraulic structures.

Testing a one-dimensional prescription of dynamical shear mixing with a two-dimensional hydrodynamic simulation

NASA Astrophysics Data System (ADS)

Edelmann, P. V. F.; Röpke, F. K.; Hirschi, R.; Georgy, C.; Jones, S.

2017-07-01

Context. The treatment of mixing processes is still one of the major uncertainties in 1D stellar evolution models. This is mostly due to the need to parametrize and approximate aspects of hydrodynamics in hydrostatic codes. In particular, the effect of hydrodynamic instabilities in rotating stars, for example, dynamical shear instability, evades consistent description. Aims: We intend to study the accuracy of the diffusion approximation to dynamical shear in hydrostatic stellar evolution models by comparing 1D models to a first-principle hydrodynamics simulation starting from the same initial conditions. Methods: We chose an initial model calculated with the stellar evolution code GENEC that is just at the onset of a dynamical shear instability but does not show any other instabilities (e.g., convection). This was mapped to the hydrodynamics code SLH to perform a 2D simulation in the equatorial plane. We compare the resulting profiles in the two codes and compute an effective diffusion coefficient for the hydro simulation. Results: Shear instabilities develop in the 2D simulation in the regions predicted by linear theory to become unstable in the 1D stellar evolution model. Angular velocity and chemical composition is redistributed in the unstable region, thereby creating new unstable regions. After a period of time, the system settles in a symmetric, steady state, which is Richardson stable everywhere in the 2D simulation, whereas the instability remains for longer in the 1D model due to the limitations of the current implementation in the 1D code. A spatially resolved diffusion coefficient is extracted by comparing the initial and final profiles of mean atomic mass. Conclusions: The presented simulation gives a first insight on hydrodynamics of shear instabilities in a real stellar environment and even allows us to directly extract an effective diffusion coefficient. We see evidence for a critical Richardson number of 0.25 as regions above this threshold remain

Hydrodynamics simulations of 2{omega} laser propagation in underdense gasbag plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meezan, N.B.; Divol, L.; Marinak, M.M.

2004-12-01

Recent 2{omega} laser propagation and stimulated Raman backscatter (SRS) experiments performed on the Helen laser have been analyzed using the radiation-hydrodynamics code HYDRA [M. M. Marinak, G. D. Kerbel, N. A. Gentile, O. Jones, D. Munro, S. Pollaine, T. R. Dittrich, and S. W. Haan, Phys. Plasmas 8, 2275 (2001)]. These experiments utilized two diagnostics sensitive to the hydrodynamics of gasbag targets: a fast x-ray framing camera (FXI) and a SRS streak spectrometer. With a newly implemented nonlocal thermal transport model, HYDRA is able to reproduce many features seen in the FXI images and the SRS streak spectra. Experimental andmore » simulated side-on FXI images suggest that propagation can be explained by classical laser absorption and the resulting hydrodynamics. Synthetic SRS spectra generated from the HYDRA results reproduce the details of the experimental SRS streak spectra. Most features in the synthetic spectra can be explained solely by axial density and temperature gradients. The total SRS backscatter increases with initial gasbag fill density up to {approx_equal}0.08 times the critical density, then decreases. Data from a near-backscatter imaging camera show that severe beam spray is not responsible for the trend in total backscatter. Filamentation does not appear to be a significant factor in gasbag hydrodynamics. The simulation and analysis techniques established here can be used in ongoing experimental campaigns on the Omega laser facility and the National Ignition Facility.« less

Simulation and experimental study of rheological properties of CeO2-water nanofluid

NASA Astrophysics Data System (ADS)

Loya, Adil; Stair, Jacqueline L.; Ren, Guogang

2015-10-01

Metal oxide nanoparticles offer great merits over controlling rheological, thermal, chemical and physical properties of solutions. The effectiveness of a nanoparticle to modify the properties of a fluid depends on its diffusive properties with respect to the fluid. In this study, rheological properties of aqueous fluids (i.e. water) were enhanced with the addition of CeO2 nanoparticles. This study was characterized by the outcomes of simulation and experimental results of nanofluids. The movement of nanoparticles in the fluidic media was simulated by a large-scale molecular thermal dynamic program (i.e. LAMMPS). The COMPASS force field was employed with smoothed particle hydrodynamic potential (SPH) and discrete particle dynamics potential (DPD). However, this study develops the understanding of how the rheological properties are affected due to the addition of nanoparticles in a fluid and the way DPD and SPH can be used for accurately estimating the rheological properties with Brownian effect. The rheological results of the simulation were confirmed by the convergence of the stress autocorrelation function, whereas experimental properties were measured using a rheometer. These rheological values of simulation were obtained and agreed within 5 % of the experimental values; they were identified and treated with a number of iterations and experimental tests. The results of the experiment and simulation show that 10 % CeO2 nanoparticles dispersion in water has a viscosity of 2.0-3.3 mPas.

What Controls Thermo-osmosis? Molecular Simulations Show the Critical Role of Interfacial Hydrodynamics

NASA Astrophysics Data System (ADS)

Fu, Li; Merabia, Samy; Joly, Laurent

2017-11-01

Thermo-osmotic and related thermophoretic phenomena can be found in many situations from biology to colloid science, but the underlying molecular mechanisms remain largely unexplored. Using molecular dynamics simulations, we measure the thermo-osmosis coefficient by both mechanocaloric and thermo-osmotic routes, for different solid-liquid interfacial energies. The simulations reveal, in particular, the crucial role of nanoscale interfacial hydrodynamics. For nonwetting surfaces, thermo-osmotic transport is largely amplified by hydrodynamic slip at the interface. For wetting surfaces, the position of the hydrodynamic shear plane plays a key role in determining the amplitude and sign of the thermo-osmosis coefficient. Finally, we measure a giant thermo-osmotic response of the water-graphene interface, which we relate to the very low interfacial friction displayed by this system. These results open new perspectives for the design of efficient functional interfaces for, e.g., waste-heat harvesting.

What Controls Thermo-osmosis? Molecular Simulations Show the Critical Role of Interfacial Hydrodynamics.

PubMed

Fu, Li; Merabia, Samy; Joly, Laurent

2017-11-24

Thermo-osmotic and related thermophoretic phenomena can be found in many situations from biology to colloid science, but the underlying molecular mechanisms remain largely unexplored. Using molecular dynamics simulations, we measure the thermo-osmosis coefficient by both mechanocaloric and thermo-osmotic routes, for different solid-liquid interfacial energies. The simulations reveal, in particular, the crucial role of nanoscale interfacial hydrodynamics. For nonwetting surfaces, thermo-osmotic transport is largely amplified by hydrodynamic slip at the interface. For wetting surfaces, the position of the hydrodynamic shear plane plays a key role in determining the amplitude and sign of the thermo-osmosis coefficient. Finally, we measure a giant thermo-osmotic response of the water-graphene interface, which we relate to the very low interfacial friction displayed by this system. These results open new perspectives for the design of efficient functional interfaces for, e.g., waste-heat harvesting.

A challenge to dSph formation models: are the most isolated Local Group dSph galaxies truly old?

NASA Astrophysics Data System (ADS)

Monelli, Matteo

2017-08-01

What is the origin of the different dwarf galaxy types? The classification into dwarf irregular (dIrr), spheroidal (dSph), and transition (dT) types is based on their present-day properties. However, star formation histories (SFHs) reconstructed from deep color-magnitude diagrams (CMDs) provide details on the early evolution of galaxies of all these types, and indicate only two basic evolutionary paths. One is characterized by a vigorous but brief initial star-forming event, and little or no star formation thereafter (fast evolution), and the other one by roughly continuous star formation until (nearly) the present time (slow evolution). These two paths do not map directly onto the dIrr, dT and dSph types. Thus, the present galaxy properties do not reflect their lifetime evolution. Since there are some indications that slow dwarfs were assembled in lower-density environments than fast dwarfs, Gallart et al (2015) proposed that the distinction between fast and slow dwarfs reflects the characteristic density of the environment where they formed. This scenario, and more generally scenarios where dSph galaxies formed through the interaction with a massive galaxy, are challenged by a small sample of extremely isolated dSph/dT in the outer fringes of the Local Group. This proposal targets two of these objects (VV124, KKR25) for which we will infer their SFH - through a novel technique that combines the information from their RR Lyrae stars and deep CMDs sampling the intermediate-age population - in order to test these scenarios. This is much less demanding on observing time than classical SFH derivation using full depth CMDs.

Structure–Activity Relationship Studies and in Vivo Activity of Guanidine-Based Sphingosine Kinase Inhibitors: Discovery of SphK1- and SphK2-Selective Inhibitors

PubMed Central

Kharel, Yugesh; Raje, Mithun R.; Gao, Ming; Tomsig, Jose L.; Lynch, Kevin R.; Santos, Webster L.

2015-01-01

Sphingosine 1-phosphate (S1P) is a pleiotropic signaling molecule that acts as a ligand for five G-protein coupled receptors (S1P1–5) whose downstream effects are implicated in a variety of important pathologies including sickle cell disease, cancer, inflammation, and fibrosis. The synthesis of S1P is catalyzed by sphingosine kinase (SphK) isoforms 1 and 2, and hence, inhibitors of this phosphorylation step are pivotal in understanding the physiological functions of SphKs. To date, SphK1 and 2 inhibitors with the potency, selectivity, and in vivo stability necessary to determine the potential of these kinases as therapeutic targets are lacking. Herein, we report the design, synthesis, and structure–activity relationship studies of guanidine-based SphK inhibitors bearing an oxadiazole ring in the scaffold. Our studies demonstrate that SLP120701, a SphK2-selective inhibitor (Ki = 1 μM), decreases S1P levels in histiocytic lymphoma (U937) cells. Surprisingly, homologation with a single methylene unit between the oxadiazole and heterocyclic ring afforded a SphK1-selective inhibitor in SLP7111228 (Ki = 48 nM), which also decreased S1P levels in cultured U937 cells. In vivo application of both compounds, however, resulted in contrasting effect in circulating levels of S1P. Administration of SLP7111228 depressed blood S1P levels while SLP120701 increased levels of S1P. Taken together, these compounds provide an in vivo chemical toolkit to interrogate the effect of increasing or decreasing S1P levels and whether such a maneuver can have implications in disease states. PMID:25643074

Meshless Lagrangian SPH method applied to isothermal lid-driven cavity flow at low-Re numbers

NASA Astrophysics Data System (ADS)

Fraga Filho, C. A. D.; Chacaltana, J. T. A.; Pinto, W. J. N.

2018-01-01

SPH is a recent particle method applied in the cavities study, without many results available in the literature. The lid-driven cavity flow is a classic problem of the fluid mechanics, extensively explored in the literature and presenting a considerable complexity. The aim of this paper is to present a solution from the Lagrangian viewpoint for this problem. The discretization of the continuum domain is performed using the Lagrangian particles. The physical laws of mass, momentum and energy conservation are presented by the Navier-Stokes equations. A serial numerical code, written in Fortran programming language, has been used to perform the numerical simulations. The application of the SPH and comparison with the literature (mesh methods and a meshless collocation method) have been done. The positions of the primary vortex centre and the non-dimensional velocity profiles passing through the geometric centre of the cavity have been analysed. The numerical Lagrangian results showed a good agreement when compared to the results found in the literature, specifically for { Re} < 100.00 . Suggestions for improvements in the SPH model presented are listed, in the search for better results for flows with higher Reynolds numbers.

Insights from Synthetic Star-forming Regions. I. Reliable Mock Observations from SPH Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koepferl, Christine M.; Robitaille, Thomas P.; Biscani, Francesco

Through synthetic observations of a hydrodynamical simulation of an evolving star-forming region, we assess how the choice of observational techniques affects the measurements of properties that trace star formation. Testing and calibrating observational measurements requires synthetic observations that are as realistic as possible. In this part of the series (Paper I), we explore different techniques for mapping the distributions of densities and temperatures from the particle-based simulations onto a Voronoi mesh suitable for radiative transfer and consequently explore their accuracy. We further test different ways to set up the radiative transfer in order to produce realistic synthetic observations. We give amore » detailed description of all methods and ultimately recommend techniques. We have found that the flux around 20 μ m is strongly overestimated when blindly coupling the dust radiative transfer temperature with the hydrodynamical gas temperature. We find that when instead assuming a constant background dust temperature in addition to the radiative transfer heating, the recovered flux is consistent with actual observations. We present around 5800 realistic synthetic observations for Spitzer and Herschel bands, at different evolutionary time-steps, distances, and orientations. In the upcoming papers of this series (Papers II, III, and IV), we will test and calibrate measurements of the star formation rate, gas mass, and the star formation efficiency using our realistic synthetic observations.« less

Prescribed Velocity Gradients for Highly Viscous SPH Fluids with Vorticity Diffusion.

PubMed

Peer, Andreas; Teschner, Matthias

2017-12-01

Working with prescribed velocity gradients is a promising approach to efficiently and robustly simulate highly viscous SPH fluids. Such approaches allow to explicitly and independently process shear rate, spin, and expansion rate. This can be used to, e.g., avoid interferences between pressure and viscosity solvers. Another interesting aspect is the possibility to explicitly process the vorticity, e.g., to preserve the vorticity. In this context, this paper proposes a novel variant of the prescribed-gradient idea that handles vorticity in a physically motivated way. In contrast to a less appropriate vorticity preservation that has been used in a previous approach, vorticity is diffused. The paper illustrates the utility of the vorticity diffusion. Therefore, comparisons of the proposed vorticity diffusion with vorticity preservation and additionally with vorticity damping are presented. The paper further discusses the relation between prescribed velocity gradients and prescribed velocity Laplacians which improves the intuition behind the prescribed-gradient method for highly viscous SPH fluids. Finally, the paper discusses the relation of the proposed method to a physically correct implicit viscosity formulation.

Transient hydrodynamic finite-size effects in simulations under periodic boundary conditions

NASA Astrophysics Data System (ADS)

Asta, Adelchi J.; Levesque, Maximilien; Vuilleumier, Rodolphe; Rotenberg, Benjamin

2017-06-01

We use lattice-Boltzmann and analytical calculations to investigate transient hydrodynamic finite-size effects induced by the use of periodic boundary conditions. These effects are inevitable in simulations at the molecular, mesoscopic, or continuum levels of description. We analyze the transient response to a local perturbation in the fluid and obtain the local velocity correlation function via linear response theory. This approach is validated by comparing the finite-size effects on the steady-state velocity with the known results for the diffusion coefficient. We next investigate the full time dependence of the local velocity autocorrelation function. We find at long times a crossover between the expected t-3 /2 hydrodynamic tail and an oscillatory exponential decay, and study the scaling with the system size of the crossover time, exponential rate and amplitude, and oscillation frequency. We interpret these results from the analytic solution of the compressible Navier-Stokes equation for the slowest modes, which are set by the system size. The present work not only provides a comprehensive analysis of hydrodynamic finite-size effects in bulk fluids, which arise regardless of the level of description and simulation algorithm, but also establishes the lattice-Boltzmann method as a suitable tool to investigate such effects in general.

Validating Semi-analytic Models of High-redshift Galaxy Formation Using Radiation Hydrodynamical Simulations

NASA Astrophysics Data System (ADS)

Côté, Benoit; Silvia, Devin W.; O’Shea, Brian W.; Smith, Britton; Wise, John H.

2018-05-01

We use a cosmological hydrodynamic simulation calculated with Enzo and the semi-analytic galaxy formation model (SAM) GAMMA to address the chemical evolution of dwarf galaxies in the early universe. The long-term goal of the project is to better understand the origin of metal-poor stars and the formation of dwarf galaxies and the Milky Way halo by cross-validating these theoretical approaches. We combine GAMMA with the merger tree of the most massive galaxy found in the hydrodynamic simulation and compare the star formation rate, the metallicity distribution function (MDF), and the age–metallicity relationship predicted by the two approaches. We found that the SAM can reproduce the global trends of the hydrodynamic simulation. However, there are degeneracies between the model parameters, and more constraints (e.g., star formation efficiency, gas flows) need to be extracted from the simulation to isolate the correct semi-analytic solution. Stochastic processes such as bursty star formation histories and star formation triggered by supernova explosions cannot be reproduced by the current version of GAMMA. Non-uniform mixing in the galaxy’s interstellar medium, coming primarily from self-enrichment by local supernovae, causes a broadening in the MDF that can be emulated in the SAM by convolving its predicted MDF with a Gaussian function having a standard deviation of ∼0.2 dex. We found that the most massive galaxy in the simulation retains nearby 100% of its baryonic mass within its virial radius, which is in agreement with what is needed in GAMMA to reproduce the global trends of the simulation.

Modeling Wind Wave Evolution from Deep to Shallow Water

DTIC Science & Technology

2014-09-30

results are very promising (see Figure 2). However, for the sake of efficiency, non-hydrostatic models assume a single-valued free surface in the...1996) are ongoing. Figure 3 Smoothed-Particle Hydrodynamics ( SPH ) simulations of waves breaking over an artificial reef in the laboratory (see... surface as predicted by the SPH model (see Dalrymple & Rogers, 2006). The agreement in the breaker dynamics predicted by the model and seen in the

Tokamak magneto-hydrodynamics and reference magnetic coordinates for simulations of plasma disruptions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zakharov, Leonid E.; Li, Xujing

This paper formulates the Tokamak Magneto-Hydrodynamics (TMHD), initially outlined by X. Li and L. E. Zakharov [Plasma Science and Technology 17(2), 97–104 (2015)] for proper simulations of macroscopic plasma dynamics. The simplest set of magneto-hydrodynamics equations, sufficient for disruption modeling and extendable to more refined physics, is explained in detail. First, the TMHD introduces to 3-D simulations the Reference Magnetic Coordinates (RMC), which are aligned with the magnetic field in the best possible way. The numerical implementation of RMC is adaptive grids. Being consistent with the high anisotropy of the tokamak plasma, RMC allow simulations at realistic, very high plasmamore » electric conductivity. Second, the TMHD splits the equation of motion into an equilibrium equation and the plasma advancing equation. This resolves the 4 decade old problem of Courant limitations of the time step in existing, plasma inertia driven numerical codes. The splitting allows disruption simulations on a relatively slow time scale in comparison with the fast time of ideal MHD instabilities. A new, efficient numerical scheme is proposed for TMHD.« less

SANTA BARBARA CLUSTER COMPARISON TEST WITH DISPH

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saitoh, Takayuki R.; Makino, Junichiro, E-mail: saitoh@elsi.jp

2016-06-01

The Santa Barbara cluster comparison project revealed that there is a systematic difference between entropy profiles of clusters of galaxies obtained by Eulerian mesh and Lagrangian smoothed particle hydrodynamics (SPH) codes: mesh codes gave a core with a constant entropy, whereas SPH codes did not. One possible reason for this difference is that mesh codes are not Galilean invariant. Another possible reason is the problem of the SPH method, which might give too much “protection” to cold clumps because of the unphysical surface tension induced at contact discontinuities. In this paper, we apply the density-independent formulation of SPH (DISPH), whichmore » can handle contact discontinuities accurately, to simulations of a cluster of galaxies and compare the results with those with the standard SPH. We obtained the entropy core when we adopt DISPH. The size of the core is, however, significantly smaller than those obtained with mesh simulations and is comparable to those obtained with quasi-Lagrangian schemes such as “moving mesh” and “mesh free” schemes. We conclude that both the standard SPH without artificial conductivity and Eulerian mesh codes have serious problems even with such an idealized simulation, while DISPH, SPH with artificial conductivity, and quasi-Lagrangian schemes have sufficient capability to deal with it.« less

Comparing cosmological hydrodynamic simulations with observations of high- redshift galaxy formation

NASA Astrophysics Data System (ADS)

Finlator, Kristian Markwart

We use cosmological hydrodynamic simulations to study the impact of outflows and radiative feedback on high-redshift galaxies. For outflows, we consider simulations that assume (i) no winds, (ii) a "constant-wind" model in which the mass-loading factor and outflow speed are constant, and (iii) "momentum-driven" winds in which both parameters vary smoothly with mass. In order to treat radiative feedback, we develop a moment-based radiative transfer technique that operates in both post-processing and coupled radiative hydrodynamic modes. We first ask how outflows impact the broadband spectral energy distributions (SEDs) of six observed reionization-epoch galaxies. Simulations reproduce five regardless of the outflow prescription, while the sixth suggests an unusually bursty star formation history. We conclude that (i) simulations broadly account for available constraints on reionization-epoch galaxies, (ii) individual SEDs do not constrain outflows, and (iii) SED comparisons efficiently isolate objects that challenge simulations. We next study how outflows impact the galaxy mass metallicity relation (MZR). Momentum-driven outflows uniquely reproduce observations at z = 2. In this scenario, galaxies obey two equilibria: (i) The rate at which a galaxy processes gas into stars and outflows tracks its inflow rate; and (ii) The gas enrichment rate owing to star formation balances the dilution rate owing to inflows. Combining these conditions indicates that the MZR is dominated by the (instantaneous) variation of outflows with mass, with more-massive galaxies driving less gas into outflows per unit stellar mass formed. Turning to radiative feedback, we use post-processing simulations to study the topology of reionization. Reionization begins in overdensities and then "leaks" directly into voids, with filaments reionizing last owing to their high density and low emissivity. This result conflicts with previous findings that voids ionize last. We argue that it owes to the

Role of sph2 Gene Regulation in Hemolytic and Sphingomyelinase Activities Produced by Leptospira interrogans.

PubMed

Narayanavari, Suneel A; Lourdault, Kristel; Sritharan, Manjula; Haake, David A; Matsunaga, James

2015-01-01

Pathogenic members of the genus Leptospira are the causative agents of leptospirosis, a neglected disease of public and veterinary health concern. Leptospirosis is a systemic disease that in its severest forms leads to renal insufficiency, hepatic dysfunction, and pulmonary failure. Many strains of Leptospira produce hemolytic and sphingomyelinase activities, and a number of candidate leptospiral hemolysins have been identified based on sequence similarity to well-characterized bacterial hemolysins. Five of the putative hemolysins are sphingomyelinase paralogs. Although recombinant forms of the sphingomyelinase Sph2 and other hemolysins lyse erythrocytes, none have been demonstrated to contribute to the hemolytic activity secreted by leptospiral cells. In this study, we examined the regulation of sph2 and its relationship to hemolytic and sphingomyelinase activities produced by several L. interrogans strains cultivated under the osmotic conditions found in the mammalian host. The sph2 gene was poorly expressed when the Fiocruz L1-130 (serovar Copenhageni), 56601 (sv. Lai), and L495 (sv. Manilae) strains were cultivated in the standard culture medium EMJH. Raising EMJH osmolarity to physiological levels with sodium chloride enhanced Sph2 production in all three strains. In addition, the Pomona subtype kennewicki strain LC82-25 produced substantially greater amounts of Sph2 during standard EMJH growth than the other strains, and sph2 expression increased further by addition of salt. When 10% rat serum was present in EMJH along with the sodium chloride supplement, Sph2 production increased further in all strains. Osmotic regulation and differences in basal Sph2 production in the Manilae L495 and Pomona strains correlated with the levels of secreted hemolysin and sphingomyelinase activities. Finally, a transposon insertion in sph2 dramatically reduced hemolytic and sphingomyelinase activities during incubation of L. interrogans at physiologic osmolarity

Numerical simulation of the hydrodynamic instabilities of Richtmyer-Meshkov and Rayleigh-Taylor

NASA Astrophysics Data System (ADS)

Fortova, S. V.; Shepelev, V. V.; Troshkin, O. V.; Kozlov, S. A.

2017-09-01

The paper presents the results of numerical simulation of the development of hydrodynamic instabilities of Richtmyer-Meshkov and Rayleigh-Taylor encountered in experiments [1-3]. For the numerical solution used the TPS software package (Turbulence Problem Solver) that implements a generalized approach to constructing computer programs for a wide range of problems of hydrodynamics, described by the system of equations of hyperbolic type. As numerical methods are used the method of large particles and ENO-scheme of the second order with Roe solver for the approximate solution of the Riemann problem.

The moving confluence route technology with WAD scheme for 3D hydrodynamic simulation in high altitude inland waters

NASA Astrophysics Data System (ADS)

Wang, Yonggui; Yang, Yinqun; Chen, Xiaolong; Engel, Bernard A.; Zhang, Wanshun

2018-04-01

For three-dimensional hydrodynamic simulations in inland waters, the rapid changes with moving boundary and various input conditions should be considered. Some models are developed with moving boundary but the dynamic change of discharges is unresolved or ignored. For better hydrodynamic simulation in inland waters, the widely used 3D model, ECOMSED, has been improved by moving confluence route (MCR) method with a wetting and drying scheme (WAD). The fixed locations of water and pollutants inputs from tributaries, point sources and non-point sources have been changed to dynamic confluence routes as the boundary moving. The improved model was applied in an inland water area, Qingshuihai reservoir, Kunming City, China, for a one-year hydrodynamic simulation. The results were verified by water level, flow velocity and water mass conservation. Detailed water level variation analysis and velocity field comparison at different times showed that the improved model has better performance for simulating the boundary moving phenomenon and moving discharges along with water level changing than the original one. The improved three-dimensional model is available for hydrodynamics simulation in water bodies where water boundary shifts along with change of water level and have various inlets.

3D hydrodynamic simulations of carbon burning in massive stars

NASA Astrophysics Data System (ADS)

Cristini, A.; Meakin, C.; Hirschi, R.; Arnett, D.; Georgy, C.; Viallet, M.; Walkington, I.

2017-10-01

We present the first detailed 3D hydrodynamic implicit large eddy simulations of turbulent convection of carbon burning in massive stars. Simulations begin with radial profiles mapped from a carbon-burning shell within a 15 M⊙ 1D stellar evolution model. We consider models with 1283, 2563, 5123, and 10243 zones. The turbulent flow properties of these carbon-burning simulations are very similar to the oxygen-burning case. We performed a mean field analysis of the kinetic energy budgets within the Reynolds-averaged Navier-Stokes framework. For the upper convective boundary region, we find that the numerical dissipation is insensitive to resolution for linear mesh resolutions above 512 grid points. For the stiffer, more stratified lower boundary, our highest resolution model still shows signs of decreasing sub-grid dissipation suggesting it is not yet numerically converged. We find that the widths of the upper and lower boundaries are roughly 30 per cent and 10 per cent of the local pressure scaleheights, respectively. The shape of the boundaries is significantly different from those used in stellar evolution models. As in past oxygen-shell-burning simulations, we observe entrainment at both boundaries in our carbon-shell-burning simulations. In the large Péclet number regime found in the advanced phases, the entrainment rate is roughly inversely proportional to the bulk Richardson number, RiB (∝RiB-α, 0.5 ≲ α ≲ 1.0). We thus suggest the use of RiB as a means to take into account the results of 3D hydrodynamics simulations in new 1D prescriptions of convective boundary mixing.

VINE-A NUMERICAL CODE FOR SIMULATING ASTROPHYSICAL SYSTEMS USING PARTICLES. I. DESCRIPTION OF THE PHYSICS AND THE NUMERICAL METHODS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wetzstein, M.; Nelson, Andrew F.; Naab, T.

2009-10-01

We present a numerical code for simulating the evolution of astrophysical systems using particles to represent the underlying fluid flow. The code is written in Fortran 95 and is designed to be versatile, flexible, and extensible, with modular options that can be selected either at the time the code is compiled or at run time through a text input file. We include a number of general purpose modules describing a variety of physical processes commonly required in the astrophysical community and we expect that the effort required to integrate additional or alternate modules into the code will be small. Inmore » its simplest form the code can evolve the dynamical trajectories of a set of particles in two or three dimensions using a module which implements either a Leapfrog or Runge-Kutta-Fehlberg integrator, selected by the user at compile time. The user may choose to allow the integrator to evolve the system using individual time steps for each particle or with a single, global time step for all. Particles may interact gravitationally as N-body particles, and all or any subset may also interact hydrodynamically, using the smoothed particle hydrodynamic (SPH) method by selecting the SPH module. A third particle species can be included with a module to model massive point particles which may accrete nearby SPH or N-body particles. Such particles may be used to model, e.g., stars in a molecular cloud. Free boundary conditions are implemented by default, and a module may be selected to include periodic boundary conditions. We use a binary 'Press' tree to organize particles for rapid access in gravity and SPH calculations. Modules implementing an interface with special purpose 'GRAPE' hardware may also be selected to accelerate the gravity calculations. If available, forces obtained from the GRAPE coprocessors may be transparently substituted for those obtained from the tree, or both tree and GRAPE may be used as a combination GRAPE/tree code. The code may be run without

Vine—A Numerical Code for Simulating Astrophysical Systems Using Particles. I. Description of the Physics and the Numerical Methods

NASA Astrophysics Data System (ADS)

Wetzstein, M.; Nelson, Andrew F.; Naab, T.; Burkert, A.

2009-10-01

We present a numerical code for simulating the evolution of astrophysical systems using particles to represent the underlying fluid flow. The code is written in Fortran 95 and is designed to be versatile, flexible, and extensible, with modular options that can be selected either at the time the code is compiled or at run time through a text input file. We include a number of general purpose modules describing a variety of physical processes commonly required in the astrophysical community and we expect that the effort required to integrate additional or alternate modules into the code will be small. In its simplest form the code can evolve the dynamical trajectories of a set of particles in two or three dimensions using a module which implements either a Leapfrog or Runge-Kutta-Fehlberg integrator, selected by the user at compile time. The user may choose to allow the integrator to evolve the system using individual time steps for each particle or with a single, global time step for all. Particles may interact gravitationally as N-body particles, and all or any subset may also interact hydrodynamically, using the smoothed particle hydrodynamic (SPH) method by selecting the SPH module. A third particle species can be included with a module to model massive point particles which may accrete nearby SPH or N-body particles. Such particles may be used to model, e.g., stars in a molecular cloud. Free boundary conditions are implemented by default, and a module may be selected to include periodic boundary conditions. We use a binary "Press" tree to organize particles for rapid access in gravity and SPH calculations. Modules implementing an interface with special purpose "GRAPE" hardware may also be selected to accelerate the gravity calculations. If available, forces obtained from the GRAPE coprocessors may be transparently substituted for those obtained from the tree, or both tree and GRAPE may be used as a combination GRAPE/tree code. The code may be run without

Numerical simulation of the hydrodynamics within octagonal tanks in recirculating aquaculture systems

NASA Astrophysics Data System (ADS)

Liu, Yao; Liu, Baoliang; Lei, Jilin; Guan, Changtao; Huang, Bin

2017-07-01

A three-dimensional numerical model was established to simulate the hydrodynamics within an octagonal tank of a recirculating aquaculture system. The realizable k- ɛ turbulence model was applied to describe the flow, the discrete phase model (DPM) was applied to generate particle trajectories, and the governing equations are solved using the finite volume method. To validate this model, the numerical results were compared with data obtained from a full-scale physical model. The results show that: (1) the realizable k- ɛ model applied for turbulence modeling describes well the flow pattern in octagonal tanks, giving an average relative error of velocities between simulated and measured values of 18% from contour maps of velocity magnitudes; (2) the DPM was applied to obtain particle trajectories and to simulate the rate of particle removal from the tank. The average relative error of the removal rates between simulated and measured values was 11%. The DPM can be used to assess the self-cleaning capability of an octagonal tank; (3) a comprehensive account of the hydrodynamics within an octagonal tank can be assessed from simulations. The velocity distribution was uniform with an average velocity of 15 cm/s; the velocity reached 0.8 m/s near the inlet pipe, which can result in energy losses and cause wall abrasion; the velocity in tank corners was more than 15 cm/s, which suggests good water mixing, and there was no particle sedimentation. The percentage of particle removal for octagonal tanks was 90% with the exception of a little accumulation of ≤ 5 mm particle in the area between the inlet pipe and the wall. This study demonstrated a consistent numerical model of the hydrodynamics within octagonal tanks that can be further used in their design and optimization as well as promote the wide use of computational fluid dynamics in aquaculture engineering.

Self-consistent Modeling of Reionization in Cosmological Hydrodynamical Simulations

DOE PAGES

Oñorbe, Jose; Hennawi, Joseph F.; Lukić, Zarija

2017-03-08

The ultraviolet background (UVB) emitted by quasars and galaxies governs the ionization and thermal state of the intergalactic medium (IGM), regulates the formation of high-redshift galaxies, and is thus a key quantity for modeling cosmic reionization. The vast majority of cosmological hydrodynamical simulations implement the UVB via a set of spatially uniform photoionization and photoheating rates derived from UVB synthesis models. In this paper, we show that simulations using canonical UVB rates reionize and, perhaps more importantly, spuriously heat the IGM, much earlier (more » $$z\\sim 15$$) than they should. This problem arises because at $$z\\gt 6$$, where observational constraints are nonexistent, the UVB amplitude is far too high. We introduce a new methodology to remedy this issue, and we generate self-consistent photoionization and photoheating rates to model any chosen reionization history. Following this approach, we run a suite of hydrodynamical simulations of different reionization scenarios and explore the impact of the timing of reionization and its concomitant heat injection on the thermal state of the IGM. We present a comprehensive study of the pressure smoothing scale of IGM gas, illustrating its dependence on the details of both hydrogen and helium reionization, and argue that it plays a fundamental role in interpreting Lyα forest statistics and the thermal evolution of the IGM. The premature IGM heating we have uncovered implies that previous work has likely dramatically overestimated the impact of photoionization feedback on galaxy formation, which sets the minimum halo mass able to form stars at high redshifts. Finally, we make our new UVB photoionization and photoheating rates publicly available for use in future simulations.« less

Self-consistent Modeling of Reionization in Cosmological Hydrodynamical Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oñorbe, Jose; Hennawi, Joseph F.; Lukić, Zarija

The ultraviolet background (UVB) emitted by quasars and galaxies governs the ionization and thermal state of the intergalactic medium (IGM), regulates the formation of high-redshift galaxies, and is thus a key quantity for modeling cosmic reionization. The vast majority of cosmological hydrodynamical simulations implement the UVB via a set of spatially uniform photoionization and photoheating rates derived from UVB synthesis models. In this paper, we show that simulations using canonical UVB rates reionize and, perhaps more importantly, spuriously heat the IGM, much earlier (more » $$z\\sim 15$$) than they should. This problem arises because at $$z\\gt 6$$, where observational constraints are nonexistent, the UVB amplitude is far too high. We introduce a new methodology to remedy this issue, and we generate self-consistent photoionization and photoheating rates to model any chosen reionization history. Following this approach, we run a suite of hydrodynamical simulations of different reionization scenarios and explore the impact of the timing of reionization and its concomitant heat injection on the thermal state of the IGM. We present a comprehensive study of the pressure smoothing scale of IGM gas, illustrating its dependence on the details of both hydrogen and helium reionization, and argue that it plays a fundamental role in interpreting Lyα forest statistics and the thermal evolution of the IGM. The premature IGM heating we have uncovered implies that previous work has likely dramatically overestimated the impact of photoionization feedback on galaxy formation, which sets the minimum halo mass able to form stars at high redshifts. Finally, we make our new UVB photoionization and photoheating rates publicly available for use in future simulations.« less

Au36(SPh)23 nanomolecules.

PubMed

Nimmala, Praneeth Reddy; Dass, Amala

2011-06-22

A new core size protected completely by an aromatic thiol, Au(36)(SPh)(23), is synthesized and characterized by MALDI-TOF mass spectrometry and UV-visible spectroscopy. The synthesis involving core size changes is studied by MS, and the complete ligand coverage by aromatic thiol group is shown by NMR.

Modeling Boulder Transport by Smooth Particle Hydrodynamics

NASA Astrophysics Data System (ADS)

Karpytchev, M.

2017-12-01

Large coastal boulders are often believed to have been transported by strong tsunami andstorm waves. Understanding and quantifying the boulder transport processes is, therefore,crucial for evaluation of strength and timing of the past tsunamis and storms. Over the last10-15 year, a series of studies have obtained estimates of basic wave parameters neededto set in motion a boulder of given size, shape and mass by using simplified paramaterizationsof fluid-particle interactions. Although, parameterizing the principal hydraulic forces drivingboulder transport was succefull in reproducing effects of several historical tsunamis, someimportant details about initiation of boulder motion and the contribution of coastal wavetransformations as well as of suspended sediment to enhancing coastal currents are still lacking.These essentially non-linear processes can be particularly important for distingushing, in everyparticular case, whether it is a storm wave or a tsunami (or both) that was capable to transportspecific boulder to a given site.In this study, we employ the Smooth Particle Hydrodynamics (SPH) method in orderto get new insights on interaction of waves with boulders in the nearshore area.We first compare the SPH predictions with available laboratory experiments and thenexplore the effects of realistic 3D coastal bathymetry, non-linear behaviour of coastal waves,boulders shape and the impact of bedload and suspended sediment on dislodgement and initiationof boulder transport.

The Aurora radiation-hydrodynamical simulations of reionization: calibration and first results

NASA Astrophysics Data System (ADS)

Pawlik, Andreas H.; Rahmati, Alireza; Schaye, Joop; Jeon, Myoungwon; Dalla Vecchia, Claudio

2017-04-01

We introduce a new suite of radiation-hydrodynamical simulations of galaxy formation and reionization called Aurora. The Aurora simulations make use of a spatially adaptive radiative transfer technique that lets us accurately capture the small-scale structure in the gas at the resolution of the hydrodynamics, in cosmological volumes. In addition to ionizing radiation, Aurora includes galactic winds driven by star formation and the enrichment of the universe with metals synthesized in the stars. Our reference simulation uses 2 × 5123 dark matter and gas particles in a box of size 25 h-1 comoving Mpc with a force softening scale of at most 0.28 h-1 kpc. It is accompanied by simulations in larger and smaller boxes and at higher and lower resolution, employing up to 2 × 10243 particles, to investigate numerical convergence. All simulations are calibrated to yield simulated star formation rate functions in close agreement with observational constraints at redshift z = 7 and to achieve reionization at z ≈ 8.3, which is consistent with the observed optical depth to reionization. We focus on the design and calibration of the simulations and present some first results. The median stellar metallicities of low-mass galaxies at z = 6 are consistent with the metallicities of dwarf galaxies in the Local Group, which are believed to have formed most of their stars at high redshifts. After reionization, the mean photoionization rate decreases systematically with increasing resolution. This coincides with a systematic increase in the abundance of neutral hydrogen absorbers in the intergalactic medium.

Detonation initiation in a model of explosive: Comparative atomistic and hydrodynamics simulations

NASA Astrophysics Data System (ADS)

Murzov, S. A.; Sergeev, O. V.; Dyachkov, S. A.; Egorova, M. S.; Parshikov, A. N.; Zhakhovsky, V. V.

2016-11-01

Here we extend consistent simulations to reactive materials by the example of AB model explosive. The kinetic model of chemical reactions observed in a molecular dynamics (MD) simulation of self-sustained detonation wave can be used in hydrodynamic simulation of detonation initiation. Kinetic coefficients are obtained by minimization of difference between profiles of species calculated from the kinetic model and observed in MD simulations of isochoric thermal decomposition with a help of downhill simplex method combined with random walk in multidimensional space of fitting kinetic model parameters.

Moving-mesh cosmology: characteristics of galaxies and haloes

NASA Astrophysics Data System (ADS)

Kereš, Dušan; Vogelsberger, Mark; Sijacki, Debora; Springel, Volker; Hernquist, Lars

2012-09-01

We discuss cosmological hydrodynamic simulations of galaxy formation performed with the new moving-mesh code AREPO, which promises higher accuracy compared with the traditional smoothed particle hydrodynamics (SPH) technique that has been widely employed for this problem. In this exploratory study, we deliberately limit the complexity of the physical processes followed by the code for ease of comparison with previous calculations, and include only cooling of gas with a primordial composition, heating by a spatially uniform ultraviolet background, and a simple subresolution model for regulating star formation in the dense interstellar medium. We use an identical set of physics in corresponding simulations carried out with the well-tested SPH code GADGET, adopting also the same high-resolution gravity solver. We are thus able to compare both simulation sets on an object-by-object basis, allowing us to cleanly isolate the impact of different hydrodynamical methods on galaxy and halo properties. In accompanying papers, Vogelsberger et al. and Sijacki et al., we focus on an analysis of the global baryonic statistics predicted by the simulation codes, and complementary idealized simulations that highlight the differences between the hydrodynamical schemes. Here we investigate their influence on the baryonic properties of simulated galaxies and their surrounding haloes. We find that AREPO leads to significantly higher star formation rates for galaxies in massive haloes and to more extended gaseous discs in galaxies, which also feature a thinner and smoother morphology than their GADGET counterparts. Consequently, galaxies formed in AREPO have larger sizes and higher specific angular momentum than their SPH correspondents. Interestingly, the more efficient cooling flows in AREPO yield higher densities and lower entropies in halo centres compared to GADGET, whereas the opposite trend is found in halo outskirts. The cooling differences leading to higher star formation rates

Brownian dynamics simulations of a flexible polymer chain which includes continuous resistance and multibody hydrodynamic interactions

NASA Astrophysics Data System (ADS)

Butler, Jason E.; Shaqfeh, Eric S. G.

2005-01-01

Using methods adapted from the simulation of suspension dynamics, we have developed a Brownian dynamics algorithm with multibody hydrodynamic interactions for simulating the dynamics of polymer molecules. The polymer molecule is modeled as a chain composed of a series of inextensible, rigid rods with constraints at each joint to ensure continuity of the chain. The linear and rotational velocities of each segment of the polymer chain are described by the slender-body theory of Batchelor [J. Fluid Mech. 44, 419 (1970)]. To include hydrodynamic interactions between the segments of the chain, the line distribution of forces on each segment is approximated by making a Legendre polynomial expansion of the disturbance velocity on the segment, where the first two terms of the expansion are retained in the calculation. Thus, the resulting linear force distribution is specified by a center of mass force, couple, and stresslet on each segment. This method for calculating the hydrodynamic interactions has been successfully used to simulate the dynamics of noncolloidal suspensions of rigid fibers [O. G. Harlen, R. R. Sundararajakumar, and D. L. Koch, J. Fluid Mech. 388, 355 (1999); J. E. Butler and E. S. G. Shaqfeh, J. Fluid Mech. 468, 204 (2002)]. The longest relaxation time and center of mass diffusivity are among the quantities calculated with the simulation technique. Comparisons are made for different levels of approximation of the hydrodynamic interactions, including multibody interactions, two-body interactions, and the "freely draining" case with no interactions. For the short polymer chains studied in this paper, the results indicate a difference in the apparent scaling of diffusivity with polymer length for the multibody versus two-body level of approximation for the hydrodynamic interactions.

A future Outlook: Web based Simulation of Hydrodynamic models

NASA Astrophysics Data System (ADS)

Islam, A. S.; Piasecki, M.

2003-12-01

Despite recent advances to present simulation results as 3D graphs or animation contours, the modeling user community still faces some shortcomings when trying to move around and analyze data. Typical problems include the lack of common platforms with standard vocabulary to exchange simulation results from different numerical models, insufficient descriptions about data (metadata), lack of robust search and retrieval tools for data, and difficulties to reuse simulation domain knowledge. This research demonstrates how to create a shared simulation domain in the WWW and run a number of models through multi-user interfaces. Firstly, meta-datasets have been developed to describe hydrodynamic model data based on geographic metadata standard (ISO 19115) that has been extended to satisfy the need of the hydrodynamic modeling community. The Extended Markup Language (XML) is used to publish this metadata by the Resource Description Framework (RDF). Specific domain ontology for Web Based Simulation (WBS) has been developed to explicitly define vocabulary for the knowledge based simulation system. Subsequently, this knowledge based system is converted into an object model using Meta Object Family (MOF). The knowledge based system acts as a Meta model for the object oriented system, which aids in reusing the domain knowledge. Specific simulation software has been developed based on the object oriented model. Finally, all model data is stored in an object relational database. Database back-ends help store, retrieve and query information efficiently. This research uses open source software and technology such as Java Servlet and JSP, Apache web server, Tomcat Servlet Engine, PostgresSQL databases, Protégé ontology editor, RDQL and RQL for querying RDF in semantic level, Jena Java API for RDF. Also, we use international standards such as the ISO 19115 metadata standard, and specifications such as XML, RDF, OWL, XMI, and UML. The final web based simulation product is deployed as

Fluctuating hydrodynamics for multiscale modeling and simulation: energy and heat transfer in molecular fluids.

PubMed

Shang, Barry Z; Voulgarakis, Nikolaos K; Chu, Jhih-Wei

2012-07-28

This work illustrates that fluctuating hydrodynamics (FHD) simulations can be used to capture the thermodynamic and hydrodynamic responses of molecular fluids at the nanoscale, including those associated with energy and heat transfer. Using all-atom molecular dynamics (MD) trajectories as the reference data, the atomistic coordinates of each snapshot are mapped onto mass, momentum, and energy density fields on Eulerian grids to generate a corresponding field trajectory. The molecular length-scale associated with finite molecule size is explicitly imposed during this coarse-graining by requiring that the variances of density fields scale inversely with the grid volume. From the fluctuations of field variables, the response functions and transport coefficients encoded in the all-atom MD trajectory are computed. By using the extracted fluid properties in FHD simulations, we show that the fluctuations and relaxation of hydrodynamic fields quantitatively match with those observed in the reference all-atom MD trajectory, hence establishing compatibility between the atomistic and field representations. We also show that inclusion of energy transfer in the FHD equations can more accurately capture the thermodynamic and hydrodynamic responses of molecular fluids. The results indicate that the proposed MD-to-FHD mapping with explicit consideration of finite molecule size provides a robust framework for coarse-graining the solution phase of complex molecular systems.

Coarse-grained hydrodynamics from correlation functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Palmer, Bruce

This paper will describe a formalism for using correlation functions between different grid cells as the basis for determining coarse-grained hydrodynamic equations for modeling the behavior of mesoscopic fluid systems. Configuration from a molecular dynamics simulation are projected onto basis functions representing grid cells in a continuum hydrodynamic simulation. Equilbrium correlation functions between different grid cells are evaluated from the molecular simulation and used to determine the evolution operator for the coarse-grained hydrodynamic system. The formalism is applied to some simple hydrodynamic cases to determine the feasibility of applying this to realistic nanoscale systems.

Implementation of Hydrodynamic Simulation Code in Shock Experiment Design for Alkali Metals

NASA Astrophysics Data System (ADS)

Coleman, A. L.; Briggs, R.; Gorman, M. G.; Ali, S.; Lazicki, A.; Swift, D. C.; Stubley, P. G.; McBride, E. E.; Collins, G.; Wark, J. S.; McMahon, M. I.

2017-10-01

Shock compression techniques enable the investigation of extreme P-T states. In order to probe off-Hugoniot regions of P-T space, target makeup and laser pulse parameters must be carefully designed. HYADES is a hydrodynamic simulation code which has been successfully utilised to simulate shock compression events and refine the experimental parameters required in order to explore new P-T states in alkali metals. Here we describe simulations and experiments on potassium, along with the techniques required to access off-Hugoniot states.

Global SWOT Data Assimilation of River Hydrodynamic Model; the Twin Simulation Test of CaMa-Flood

NASA Astrophysics Data System (ADS)

Ikeshima, D.; Yamazaki, D.; Kanae, S.

2016-12-01

CaMa-Flood is a global scale model for simulating hydrodynamics in large scale rivers. It can simulate river hydrodynamics such as river discharge, flooded area, water depth and so on by inputting water runoff derived from land surface model. Recently many improvements at parameters or terrestrial data are under process to enhance the reproducibility of true natural phenomena. However, there are still some errors between nature and simulated result due to uncertainties in each model. SWOT (Surface water and Ocean Topography) is a satellite, which is going to be launched in 2021, can measure open water surface elevation. SWOT observed data can be used to calibrate hydrodynamics model at river flow forecasting and is expected to improve model's accuracy. Combining observation data into model to calibrate is called data assimilation. In this research, we developed data-assimilated river flow simulation system in global scale, using CaMa-Flood as river hydrodynamics model and simulated SWOT as observation data. Generally at data assimilation, calibrating "model value" with "observation value" makes "assimilated value". However, the observed data of SWOT satellite will not be available until its launch in 2021. Instead, we simulated the SWOT observed data using CaMa-Flood. Putting "pure input" into CaMa-Flood produce "true water storage". Extracting actual daily swath of SWOT from "true water storage" made simulated observation. For "model value", we made "disturbed water storage" by putting "noise disturbed input" to CaMa-Flood. Since both "model value" and "observation value" are made by same model, we named this twin simulation. At twin simulation, simulated observation of "true water storage" is combined with "disturbed water storage" to make "assimilated value". As the data assimilation method, we used ensemble Kalman filter. If "assimilated value" is closer to "true water storage" than "disturbed water storage", the data assimilation can be marked effective. Also

Experiment and simulation study of laser dicing silicon with water-jet

NASA Astrophysics Data System (ADS)

Bao, Jiading; Long, Yuhong; Tong, Youqun; Yang, Xiaoqing; Zhang, Bin; Zhou, Zupeng

2016-11-01

Water-jet laser processing is an internationally advanced technique, which combines the advantages of laser processing with water jet cutting. In the study, the experiment of water-jet laser dicing are conducted with ns pulsed laser of 1064 nm irradiating, and Smooth Particle Hydrodynamic (SPH) technique by AUTODYN software was modeled to research the fluid dynamics of water and melt when water jet impacting molten material. The silicon surface morphology of the irradiated spots has an appearance as one can see in porous formation. The surface morphology exhibits a large number of cavities which indicates as bubble nucleation sites. The observed surface morphology shows that the explosive melt expulsion could be a dominant process for the laser ablating silicon in liquids with nanosecond pulse laser of 1064 nm irradiating. Self-focusing phenomenon was found and its causes are analyzed. Smooth Particle Hydrodynamic (SPH) modeling technique was employed to understand the effect of water and water-jet on debris removal during water-jet laser machining.

Hydrodynamical simulations of Pinwheel nebula WR 104

NASA Astrophysics Data System (ADS)

Lamberts, A.; Fromang, S.; Dubus, G.

2010-12-01

The interaction of stellar winds from two companion stars leads to the formation of a shocked structure. Several analytic solutions have been developped to model this phenomenon. We compare our 2D and 3D hydrodynamical simulations to these results and highlight their shortcomings. Analytic solutions do not take orbital motion into account although this drastically changes the structure at large distances, turning it into a spiral. This is observed in Pinwheel Nebulae, binaries composed of a Wolf-Rayet star and an early-type star. Their infrared emission is due to dust whose origin is stil poorly constrained. We perform large scale 2D simulations of one particular system, WR 104. Including the orbital motion, we follow the flow up to a few steps of the spiral. This is made possible using adaptive mesh refinement. We determine the properties of the gas in the winds and confirm the flow in the spiral has a ballistic motion.

D Hydrodynamics Simulation of Amazonian Seasonally Flooded Wetlands

NASA Astrophysics Data System (ADS)

Pinel, S. S.; Bonnet, M. P.; Da Silva, J. S.; Cavalcanti, R., Sr.; Calmant, S.

2016-12-01

In the low Amazonian basin, interactions between floodplains and river channels are important in terms of water exchanges, sediments, or nutrients. These wetlands are considered as hotspot of biodiversity and are among the most productive in the world. However, they are threatened by climatic changes and anthropic activities. Hence, considering the implications for predicting inundation status of floodplain habitats, the strong interactions between water circulation, energy fluxes, biogeochemical and ecological processes, detailed analyses of flooding dynamics are useful and needed. Numerical inundation models offer means to study the interactions among different water sources. Modeling floods events in this area is challenging because flows respond to dynamic hydraulic controls coming from several water sources, complex geomorphology, and vegetation. In addition, due to the difficulty of access, there is a lack of existing hydrological data. In this context, the use of monitoring systems by remote sensing is a good option. In this study, we simulated filling and drainage processes of an Amazon floodplain (Janauacá Lake, AM, Brazil) over a 6 years period (2006-2012). Common approaches of flow modeling in the Amazon region consist of coupling a 1D simulation of the main channel flood wave to a 2D simulation of the inundation of the floodplain. Here, our approach differs as the floodplain is fully simulated. Model used is the 3D model IPH-ECO, which consists of a three-dimensional hydrodynamic module coupled with an ecosystem module. The IPH-ECO hydrodynamic module solves the Reynolds-Averaged Navier-Stokes equations using a semi-implicit discretization. After having calibrated the simulation against roughness coefficients, we validated the model in terms of vertical accuracy against water levels (daily in situ and altimetrics data), in terms of flood extent against inundation maps deduced from available remote-sensed product imagery (ALOS-1/PALSAR.), and in terms

Numerical simulations of regolith sampling processes

NASA Astrophysics Data System (ADS)

Schäfer, Christoph M.; Scherrer, Samuel; Buchwald, Robert; Maindl, Thomas I.; Speith, Roland; Kley, Wilhelm

2017-07-01

We present recent improvements in the simulation of regolith sampling processes in microgravity using the numerical particle method smooth particle hydrodynamics (SPH). We use an elastic-plastic soil constitutive model for large deformation and failure flows for dynamical behaviour of regolith. In the context of projected small body (asteroid or small moons) sample return missions, we investigate the efficiency and feasibility of a particular material sampling method: Brushes sweep material from the asteroid's surface into a collecting tray. We analyze the influence of different material parameters of regolith such as cohesion and angle of internal friction on the sampling rate. Furthermore, we study the sampling process in two environments by varying the surface gravity (Earth's and Phobos') and we apply different rotation rates for the brushes. We find good agreement of our sampling simulations on Earth with experiments and provide estimations for the influence of the material properties on the collecting rate.

Hydrodynamic Simulations of Unevenly Irradiated Jovian Planets

NASA Astrophysics Data System (ADS)

Langton, Jonathan; Laughlin, Gregory

2008-02-01

We employ a two-dimensional, grid-based hydrodynamic model to simulate upper atmospheric dynamics on extrasolar giant planets. The hydrodynamic equations of motion are integrated on a rotating, irradiated sphere using a pseudospectral algorithm. We use a two-frequency, two-stream approximation of radiative transfer to model the temperature forcing. This model is well suited to simulate the dynamics of the atmospheres of planets with high orbital eccentricity, which are subject to widely varying irradiation conditions. We identify six such planets, with eccentricities between e = 0.28 and e = 0.93 and semimajor axes from a = 0.0508 AU to a = 0.432 AU, as particularly interesting. For each, we determine the temperature profile and resulting infrared light curves in the 8 μm Spitzer band. Especially notable are the results for HD 80606b, which has the largest eccentricity (e = 0.9321) of any known planet, and HAT-P-2b, which transits its parent star, so that its physical properties are well constrained. Despite the varied orbital parameters, the atmospheric dynamics of these planets display a number of interesting common properties. In all cases, the atmospheric response is primarily driven by the intense irradiation at periastron. The resulting expansion of heated air produces high-velocity turbulent flow, including long-lived circumpolar vortices. In addition, a superrotating acoustic front develops on some planets; the strength of this disturbance depends on both the eccentricity and the temperature gradient from uneven heating. The specifics of the resulting infrared light curves depend strongly on the orbital geometry. We show, however, that the variations on HD 80606b and HAT-P-2b should be readily detectable at 4.5 and 8 μm using Spitzer. These two objects present the most attractive observational targets of all known high-e exoplanets.

Identification of a Serine Proteinase Homolog (Sp-SPH) Involved in Immune Defense in the Mud Crab Scylla paramamosain

PubMed Central

Zhang, Qiu-xia; Liu, Hai-peng; Chen, Rong-yuan; Shen, Kai-li; Wang, Ke-jian

2013-01-01

Clip domain serine proteinase homologs are involved in many biological processes including immune response. To identify the immune function of a serine proteinase homolog (Sp-SPH), originally isolated from hemocytes of the mud crab, Scylla paramamosain, the Sp-SPH was expressed recombinantly and purified for further studies. It was found that the Sp-SPH protein could bind to a number of bacteria (including Aeromonas hydrophila, Escherichia coli, Staphylococcus aureus, Vibrio fluvialis, Vibrio harveyi and Vibrio parahemolyticus), bacterial cell wall components such as lipopolysaccharide or peptidoglycan (PGN), and β-1, 3-glucan of fungus. But no direct antibacterial activity of Sp-SPH protein was shown by using minimum inhibitory concentration or minimum bactericidal concentration assays. Nevertheless, the Sp-SPH protein was found to significantly enhance the crab hemocyte adhesion activity (paired t-test, P<0.05), and increase phenoloxidase activity if triggered by PGN in vitro (paired t-test, P<0.05). Importantly, the Sp-SPH protein was demonstrated to promote the survival rate of the animals after challenge with A. hydrophila or V. parahemolyticus which were both recognized by Sp-SPH protein, if pre-incubated with Sp-SPH protein, respectively. Whereas, the crabs died much faster when challenged with Vibrio alginolyiicus, a pathogenic bacterium not recognized by Sp-SPH protein, compared to those of crabs challenged with A. hydrophila or V. parahemolyticus when pre-coated with Sp-SPH protein. Taken together, these data suggested that Sp-SPH molecule might play an important role in immune defense against bacterial infection in the mud crab S. paramamosain. PMID:23724001

Identification of a serine proteinase homolog (Sp-SPH) involved in immune defense in the mud crab Scylla paramamosain.

PubMed

Zhang, Qiu-xia; Liu, Hai-peng; Chen, Rong-yuan; Shen, Kai-li; Wang, Ke-jian

2013-01-01

Clip domain serine proteinase homologs are involved in many biological processes including immune response. To identify the immune function of a serine proteinase homolog (Sp-SPH), originally isolated from hemocytes of the mud crab, Scylla paramamosain, the Sp-SPH was expressed recombinantly and purified for further studies. It was found that the Sp-SPH protein could bind to a number of bacteria (including Aeromonas hydrophila, Escherichia coli, Staphylococcus aureus, Vibrio fluvialis, Vibrio harveyi and Vibrio parahemolyticus), bacterial cell wall components such as lipopolysaccharide or peptidoglycan (PGN), and β-1, 3-glucan of fungus. But no direct antibacterial activity of Sp-SPH protein was shown by using minimum inhibitory concentration or minimum bactericidal concentration assays. Nevertheless, the Sp-SPH protein was found to significantly enhance the crab hemocyte adhesion activity (paired t-test, P<0.05), and increase phenoloxidase activity if triggered by PGN in vitro (paired t-test, P<0.05). Importantly, the Sp-SPH protein was demonstrated to promote the survival rate of the animals after challenge with A. hydrophila or V. parahemolyticus which were both recognized by Sp-SPH protein, if pre-incubated with Sp-SPH protein, respectively. Whereas, the crabs died much faster when challenged with Vibrio alginolyiicus, a pathogenic bacterium not recognized by Sp-SPH protein, compared to those of crabs challenged with A. hydrophila or V. parahemolyticus when pre-coated with Sp-SPH protein. Taken together, these data suggested that Sp-SPH molecule might play an important role in immune defense against bacterial infection in the mud crab S. paramamosain.

Integration of SPH Students with Non-Handicapped Peers at Pine Ridge Center.

ERIC Educational Resources Information Center

Pegnatore, Linda A.

A 9-week practicum was designed to integrate severely/profoundly handicapped (SPH) students with third-grade nonhandicapped peer tutors in Broward County, Florida. Additional Objectives were to promote greater understanding of handicaps by nonhandicapped peer tutors and to increase awareness by SPH teachers of the importance of interactions…

Zebrafish U6 small nuclear RNA gene promoters contain a SPH element in an unusual location.

PubMed

Halbig, Kari M; Lekven, Arne C; Kunkel, Gary R

2008-09-15

Promoters for vertebrate small nuclear RNA (snRNA) genes contain a relatively simple array of transcriptional control elements, divided into proximal and distal regions. Most of these genes are transcribed by RNA polymerase II (e.g., U1, U2), whereas the U6 gene is transcribed by RNA polymerase III. Previously identified vertebrate U6 snRNA gene promoters consist of a proximal sequence element (PSE) and TATA element in the proximal region, plus a distal region with octamer (OCT) and SphI postoctamer homology (SPH) elements. We have found that zebrafish U6 snRNA promoters contain the SPH element in a novel proximal position immediately upstream of the TATA element. The zebrafish SPH element is recognized by SPH-binding factor/selenocysteine tRNA gene transcription activating factor/zinc finger protein 143 (SBF/Staf/ZNF143) in vitro. Furthermore, a zebrafish U6 promoter with a defective SPH element is inefficiently transcribed when injected into embryos.

Brownian dynamics simulations of a flexible polymer chain which includes continuous resistance and multibody hydrodynamic interactions.

PubMed

Butler, Jason E; Shaqfeh, Eric S G

2005-01-01

Using methods adapted from the simulation of suspension dynamics, we have developed a Brownian dynamics algorithm with multibody hydrodynamic interactions for simulating the dynamics of polymer molecules. The polymer molecule is modeled as a chain composed of a series of inextensible, rigid rods with constraints at each joint to ensure continuity of the chain. The linear and rotational velocities of each segment of the polymer chain are described by the slender-body theory of Batchelor [J. Fluid Mech. 44, 419 (1970)]. To include hydrodynamic interactions between the segments of the chain, the line distribution of forces on each segment is approximated by making a Legendre polynomial expansion of the disturbance velocity on the segment, where the first two terms of the expansion are retained in the calculation. Thus, the resulting linear force distribution is specified by a center of mass force, couple, and stresslet on each segment. This method for calculating the hydrodynamic interactions has been successfully used to simulate the dynamics of noncolloidal suspensions of rigid fibers [O. G. Harlen, R. R. Sundararajakumar, and D. L. Koch, J. Fluid Mech. 388, 355 (1999); J. E. Butler and E. S. G. Shaqfeh, J. Fluid Mech. 468, 204 (2002)]. The longest relaxation time and center of mass diffusivity are among the quantities calculated with the simulation technique. Comparisons are made for different levels of approximation of the hydrodynamic interactions, including multibody interactions, two-body interactions, and the "freely draining" case with no interactions. For the short polymer chains studied in this paper, the results indicate a difference in the apparent scaling of diffusivity with polymer length for the multibody versus two-body level of approximation for the hydrodynamic interactions. (c) 2005 American Institute of Physics.

A serine proteinase homologue, SPH-3, plays a central role in insect immunity.

PubMed

Felföldi, Gabriella; Eleftherianos, Ioannis; Ffrench-Constant, Richard H; Venekei, István

2011-04-15

Numerous vertebrate and invertebrate genes encode serine proteinase homologues (SPHs) similar to members of the serine proteinase family, but lacking one or more residues of the catalytic triad. These SPH proteins are thought to play a role in immunity, but their precise functions are poorly understood. In this study, we show that SPH-3 (an insect non-clip domain-containing SPH) is of central importance in the immune response of a model lepidopteran, Manduca sexta. We examine M. sexta infection with a virulent, insect-specific, Gram-negative bacterium Photorhabdus luminescens. RNA interference suppression of bacteria-induced SPH-3 synthesis severely compromises the insect's ability to defend itself against infection by preventing the transcription of multiple antimicrobial effector genes, but, surprisingly, not the transcription of immune recognition genes. Upregulation of the gene encoding prophenoloxidase and the activity of the phenoloxidase enzyme are among the antimicrobial responses that are severely attenuated on SPH-3 knockdown. These findings suggest the existence of two largely independent signaling pathways controlling immune recognition by the fat body, one governing effector gene transcription, and the other regulating genes encoding pattern recognition proteins.

RCB stars from double degenerate white dwarf mergers

NASA Astrophysics Data System (ADS)

Staff, Jan; Wiggins, Brandon K.; Marcello, Dominic; Motl, Patrick; Clayton, Geoffrey C.

2018-01-01

We have conducted grid based and SPH based hydrodynamic simulations of white dwarf mergers, to investigate the role of dredge-up and mixing during the merger. The goal is to test if sufficiently little 16O can be brought up to the surface to explain the observed 16O to 18O ratio of order unity found in RCB stars. In all simulations, the total mass is ~< 1 M⊙. By initializing both the grid based and the SPH simulations with the same setup, we can compare the results from these different methods. In most of the simulations, more than 0.01 M⊙ of 16O is brought up to the surface. Hence a similar mass of 18O must be produced in order to explain the observed oxygen ratio. However,in SPH simulations where the accretor is a hybrid He/CO white dwarf, much less 16O is brought to the surface, making this an excellent candidate for the progenitor of RCB stars.

Resolved granular debris-flow simulations with a coupled SPH-DCDEM model

NASA Astrophysics Data System (ADS)

Birjukovs Canelas, Ricardo; Domínguez, José M.; Crespo, Alejandro J. C.; Gómez-Gesteira, Moncho; Ferreira, Rui M. L.

2016-04-01

Debris flows represent some of the most relevant phenomena in geomorphological events. Due to the potential destructiveness of such flows, they are the target of a vast amount of research (Takahashi, 2007 and references therein). A complete description of the internal processes of a debris-flow is however still an elusive achievement, explained by the difficulty of accurately measuring important quantities in these flows and developing a comprehensive, generalized theoretical framework capable of describing them. This work addresses the need for a numerical model applicable to granular-fluid mixtures featuring high spatial and temporal resolution, thus capable of resolving the motion of individual particles, including all interparticle contacts. This corresponds to a brute-force approach: by applying simple interaction laws at local scales the macro-scale properties of the flow should be recovered by upscaling. This methodology effectively bypasses the complexity of modelling the intermediate scales by resolving them directly. The only caveat is the need of high performance computing, a demanding but engaging research challenge. The DualSPHysics meshless numerical implementation, based on Smoothed Particle Hydrodynamics (SPH), is expanded with a Distributed Contact Discrete Element Method (DCDEM) in order to explicitly solve the fluid and the solid phase. The model numerically solves the Navier-Stokes and continuity equations for the liquid phase and Newton's motion equations for solid bodies. The interactions between solids are modelled with classical DEM approaches (Kruggel-Emden et al, 2007). Among other validation tests, an experimental set-up for stony debris flows in a slit check dam is reproduced numerically, where solid material is introduced trough a hopper assuring a constant solid discharge for the considered time interval. With each sediment particle undergoing tens of possible contacts, several thousand time-evolving contacts are efficiently treated

Hydrodynamic Simulations of Kepler's Supernova Remnant

NASA Astrophysics Data System (ADS)

Sullivan, Jessica; Blondin, John; Borkowski, Kazik; Reynolds, Stephen

2018-01-01

Kepler’s supernova remnant contains unusual features that strongly suggest an origin in a single-degenerate Type Ia explosion, including anisotropic circumstellar medium (CSM), a strong brightness gradient, and spatially varying expansion proper motions. We present 3Dhydrodynamic simulations to test a picture in which Kepler's progenitor binary emitted a strong asymmetric wind, densest in the orbital plane, while the system moved at high velocity through the ISM. We simulate the creation of the presupernova environment as well as the supernova blast wave, using the VH-1 grid-based hydrodynamics code. We first modeled an anisotropic wind to create an asymmetric bowshock around the progenitor, then the blast wave from thesupernova. The final simulation places both previous model pieces onto a single grid and allows the blast wave to expand into the bowshock. Models were completed on a Yin-Yang grids with matching angular resolutions. By manipulating parameters that control the asymmetry of the system, we attempted to find conditions that recreated the current state of Kepler. We analyzed these models by comparing images of Kepler from the Chandra X-ray Observatory to line-of-sight projections from the model results. We also present comparisons of simulated expansion velocities with recent observations of X-ray proper motions from Chandra images. We were able to produce models that contained similar features to those seen in Kepler. We find the greatest resemblance to Kepler images with a presupernova wind with an equator-to-pole density contrast of 3 and a moderately disk-like CSM at a 5° angle between equatorial plane and system motion.

Galactic scale gas flows in colliding galaxies: 3-dimensional, N-body/hydrodynamics experiments

NASA Technical Reports Server (NTRS)

Lamb, Susan A.; Gerber, Richard A.; Balsara, Dinshaw S.

1994-01-01

We present some results from three dimensional computer simulations of collisions between models of equal mass galaxies, one of which is a rotating, disk galaxy containing both gas and stars and the other is an elliptical containing stars only. We use fully self consistent models in which the halo mass is 2.5 times that of the disk. In the experiments we have varied the impact parameter between zero (head on) and 0.9R (where R is the radius of the disk), for impacts perpendicular to the disk plane. The calculations were performed on a Cray 2 computer using a combined N-body/smooth particle hydrodynamics (SPH) program. The results show the development of complicated flows and shock structures in the direction perpendicular to the plane of the disk and the propagation outwards of a density wave in both the stars and the gas. The collisional nature of the gas results in a sharper ring than obtained for the star particles, and the development of high volume densities and shocks.

CHOLLA: A New Massively Parallel Hydrodynamics Code for Astrophysical Simulation

NASA Astrophysics Data System (ADS)

Schneider, Evan E.; Robertson, Brant E.

2015-04-01

We present Computational Hydrodynamics On ParaLLel Architectures (Cholla ), a new three-dimensional hydrodynamics code that harnesses the power of graphics processing units (GPUs) to accelerate astrophysical simulations. Cholla models the Euler equations on a static mesh using state-of-the-art techniques, including the unsplit Corner Transport Upwind algorithm, a variety of exact and approximate Riemann solvers, and multiple spatial reconstruction techniques including the piecewise parabolic method (PPM). Using GPUs, Cholla evolves the fluid properties of thousands of cells simultaneously and can update over 10 million cells per GPU-second while using an exact Riemann solver and PPM reconstruction. Owing to the massively parallel architecture of GPUs and the design of the Cholla code, astrophysical simulations with physically interesting grid resolutions (≳2563) can easily be computed on a single device. We use the Message Passing Interface library to extend calculations onto multiple devices and demonstrate nearly ideal scaling beyond 64 GPUs. A suite of test problems highlights the physical accuracy of our modeling and provides a useful comparison to other codes. We then use Cholla to simulate the interaction of a shock wave with a gas cloud in the interstellar medium, showing that the evolution of the cloud is highly dependent on its density structure. We reconcile the computed mixing time of a turbulent cloud with a realistic density distribution destroyed by a strong shock with the existing analytic theory for spherical cloud destruction by describing the system in terms of its median gas density.

Incompressible SPH (ISPH) with fast Poisson solver on a GPU

NASA Astrophysics Data System (ADS)

Chow, Alex D.; Rogers, Benedict D.; Lind, Steven J.; Stansby, Peter K.

2018-05-01

This paper presents a fast incompressible SPH (ISPH) solver implemented to run entirely on a graphics processing unit (GPU) capable of simulating several millions of particles in three dimensions on a single GPU. The ISPH algorithm is implemented by converting the highly optimised open-source weakly-compressible SPH (WCSPH) code DualSPHysics to run ISPH on the GPU, combining it with the open-source linear algebra library ViennaCL for fast solutions of the pressure Poisson equation (PPE). Several challenges are addressed with this research: constructing a PPE matrix every timestep on the GPU for moving particles, optimising the limited GPU memory, and exploiting fast matrix solvers. The ISPH pressure projection algorithm is implemented as 4 separate stages, each with a particle sweep, including an algorithm for the population of the PPE matrix suitable for the GPU, and mixed precision storage methods. An accurate and robust ISPH boundary condition ideal for parallel processing is also established by adapting an existing WCSPH boundary condition for ISPH. A variety of validation cases are presented: an impulsively started plate, incompressible flow around a moving square in a box, and dambreaks (2-D and 3-D) which demonstrate the accuracy, flexibility, and speed of the methodology. Fragmentation of the free surface is shown to influence the performance of matrix preconditioners and therefore the PPE matrix solution time. The Jacobi preconditioner demonstrates robustness and reliability in the presence of fragmented flows. For a dambreak simulation, GPU speed ups demonstrate up to 10-18 times and 1.1-4.5 times compared to single-threaded and 16-threaded CPU run times respectively.

Coarse-grained hydrodynamics from correlation functions

NASA Astrophysics Data System (ADS)

Palmer, Bruce

2018-02-01

This paper will describe a formalism for using correlation functions between different grid cells as the basis for determining coarse-grained hydrodynamic equations for modeling the behavior of mesoscopic fluid systems. Configurations from a molecular dynamics simulation or other atomistic simulation are projected onto basis functions representing grid cells in a continuum hydrodynamic simulation. Equilibrium correlation functions between different grid cells are evaluated from the molecular simulation and used to determine the evolution operator for the coarse-grained hydrodynamic system. The formalism is demonstrated on a discrete particle simulation of diffusion with a spatially dependent diffusion coefficient. Correlation functions are calculated from the particle simulation and the spatially varying diffusion coefficient is recovered using a fitting procedure.

Hydrodynamic mode associated with the pinch flow in RFP simulations

NASA Astrophysics Data System (ADS)

Delzanno, Gian Luca; Chacon, Luis; Finn, John

2007-11-01

We present a systematic study of single helicity (SH) states and quasi-single helicity (QSH) states in RFPs. We begin with cylindrical paramagnetic pinch equilibria with uniform resistivity, characterized by a single dimensionless parameter proportional to the toroidal electric field, or the RFP toroidal current parameter θ. For sufficiently high θ, there are several unstable m=1 ideal MHD instabilities, typically one of which is nonresonant, with 1/n just above q(r=0). We evolve these modes nonlinearly to saturation for low Hartmann number H. We show the existence of a new class of unstable modes [1], besides the electromagnetic kink modes typically responsible for the reversal of the axial magnetic field at the edge in RFPs. This new instability is hydrodynamic in nature and is due to the inward equilibrium pinch flow and suitable boundary conditions. In these circumstances, the total angular momentum of the system must grow in response to the flux of particles coming from the boundary. The hydrodynamic mode dominates the nonlinear phase of the velocity field but has little effect on the dynamics of the magnetic field. [1] G.L. Delzanno, L. Chac'on, J.M. Finn, Hydrodynamic mode associated with the pinch flow in Reversed Field Pinch simulations, submitted (2007).

Polymeric cobalt(ii) thiolato complexes - syntheses, structures and properties of [Co(SMes)2] and [Co(SPh)2NH3].

PubMed

Eichhöfer, Andreas; Buth, Gernot

2016-11-01

Reactions of [Co(N(SiMe 3 ) 2 ) 2 thf] with 2.1 equiv. of MesSH (Mes = C 6 H 2 -2,4,6-(CH 3 ) 3 ) yield dark brown crystals of the one dimensional chain compound [Co(SMes) 2 ]. In contrast reactions of [Co(N(SiMe 3 ) 2 ) 2 thf] with 2.1 equiv. of PhSH result in the formation of a dark brown almost X-ray amorphous powder of 'Co(SPh) 2 '. Addition of aliquots of CH 3 OH to the latter reaction resulted in the almost quantitative formation of crystalline ammonia thiolato complexes either [Co(SPh) 2 (NH 3 ) 2 ] or [Co(SPh) 2 NH 3 ]. Single crystal XRD reveals that [Co(SPh) 2 NH 3 ] forms one-dimensional chains in the crystal via μ 2 -SPh bridges whereas [Co(SPh) 2 (NH 3 ) 2 ] consists at a first glance of isolated distorted tetrahedral units. Magnetic measurements suggest strong antiferromagnetic coupling for the two chain compounds [Co(SMes) 2 ] (J = -38.6 cm -1 ) and [Co(SPh) 2 NH 3 ] (J = -27.1 cm -1 ). Interestingly, also the temperature dependence of the susceptibility of tetrahedral [Co(SPh) 2 (NH 3 ) 2 ] shows an antiferromagnetic transition at around 6 K. UV-Vis-NIR spectra display d-d bands in the NIR region between 500 and 2250 nm. Thermal gravimetric analysis of [Co(SPh) 2 (NH 3 ) 2 ] and [Co(SPh) 2 NH 3 ] reveals two well separated cleavage processes for NH 3 and SPh 2 upon heating accompanied by the stepwise formation of 'Co(SPh) 2 ' and cobalt sulfide.

Smooth particle hydrodynamic modeling and validation for impact bird substitution

NASA Astrophysics Data System (ADS)

Babu, Arun; Prasad, Ganesh

2018-04-01

Bird strike events incidentally occur and can at times be fatal for air frame structures. Federal Aviation Regulations (FAR) and such other ones mandates aircrafts to be modeled to withstand various levels of bird hit damages. The subject matter of this paper is numerical modeling of a soft body geometry for realistically substituting an actual bird for carrying out simulations of bird hit on target structures. Evolution of such a numerical code to effect an actual bird behavior through impact is much desired for making use of the state of the art computational facilities in simulating bird strike events. Validity, of simulations depicting bird hits, is largely dependent on the correctness of the bird model. In an impact, a set of complex and coupled dynamic interaction exists between the target and the impactor. To simplify this problem, impactor response needs to be decoupled from that of the target. This can be done by assuming and modeling the target as noncompliant. Bird is assumed as fluidic in a impact. Generated stresses in the bird body are significant than its yield stresses. Hydrodynamic theory is most ideal for describing this problem. Impactor literally flows steadily over the target for most part of this problem. The impact starts with an initial shock and falls into a radial release shock regime. Subsequently a steady flow is established in the bird body and this phase continues till the whole length of the bird body is turned around. Initial shock pressure and steady state pressure are ideal variables for comparing and validating the bird model. Spatial discretization of the bird is done using Smooth Particle Hydrodynamic (SPH) approach. This Discrete Element Model (DEM) offers significant advantages over other contemporary approaches. Thermodynamic state variable relations are established using Polynomial Equation of State (EOS). ANSYS AUTODYN is used to perform the explicit dynamic simulation of the impact event. Validation of the shock and steady

Optical properties of trinuclear metal chalcogenolate complexes - room temperature NIR fluorescence in [Cu2Ti(SPh)6(PPh3)2].

PubMed

Kühn, Michael; Lebedkin, Sergei; Weigend, Florian; Eichhöfer, Andreas

2017-01-31

The optical properties of four isostructural trinuclear chalcogenolato bridged metal complexes [Cu 2 Sn(SPh) 6 (PPh 3 ) 2 ], [Cu 2 Sn(SePh) 6 (PPh 3 ) 2 ], [Ag 2 Sn(SPh) 6 (PPh 3 ) 2 ] and [Cu 2 Ti(SPh) 6 (PPh 3 ) 2 ] have been investigated by absorption and photoluminescence spectroscopy and time-dependent density functional theory (TDDFT) calculations. All copper-tin compounds demonstrate near-infrared (NIR) phosphorescence at ∼900-1100 nm in the solid state at low temperature, which is nearly absent at ambient temperature. Stokes shifts of these emissions are found to be unusually large with values of about 1.5 eV. The copper-titanium complex [Cu 2 Ti(SPh) 6 (PPh 3 ) 2 ] also shows luminescence in the NIR at 1090 nm but with a much faster decay (τ ∼ 10 ns at 150 K) and a much smaller Stokes shift (ca. 0.3 eV). Even at 295 K this fluorescence is found to comprise a quantum yield as high as 9.5%. The experimental electronic absorption spectra well correspond to the spectra simulated from the calculated singlet transitions. In line with the large Stokes shifts of the emission spectra the calculations reveal for the copper-tin complexes strong structural relaxation of the excited triplet states whereas those effects are found to be much smaller in the case of the copper-titanium complex.

Molecular definition of red cell Rh haplotypes by tightly linked SphI RFLPs.

PubMed

Huang, C H; Reid, M E; Chen, Y; Coghlan, G; Okubo, Y

1996-01-01

The Rh blood group system of human red cells contains five major antigens D, C/c, and E/e (the latter four designated "non-D") that are specified by eight gene complexes known as Rh haplotypes. In this paper, we report on the mapping of RH locus and identification of a set of SphI RFLPs that are tightly linked with the Rh structural genes. Using exon-specific probes, we have localized the SphI cleavage sites resulting in these DNA markers and derived a comprehensive map for the RH locus. It was found that the SphI fragments encompassing exons 4-7 of the Rh genes occur in four banding patterns or frameworks that correspond to the distribution and segregation of the common Rh haplotypes. This linkage disequilibrium allowed a genotype-phenotype correlation and direct determination of Rh zygosity related to the Rh-positive or Rh-negative status (D/D, D/d, and d/d). Studies on the occurrence of SphI RFLPs in a number of rare Rh variants indicated that Rh phenotypic diversity has taken place on different haplotype backgrounds and has arisen by diverse genetic mechanisms. The molecular definition of Rh haplotypes by SphI RFLP frameworks should provide a useful procedure for genetic counseling and prenatal assessment of Rh alloimmunization.

VALIDITY OF HYDROSTATIC EQUILIBRIUM IN GALAXY CLUSTERS FROM COSMOLOGICAL HYDRODYNAMICAL SIMULATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suto, Daichi; Suto, Yasushi; Kawahara, Hajime

2013-04-10

We examine the validity of the hydrostatic equilibrium (HSE) assumption for galaxy clusters using one of the highest-resolution cosmological hydrodynamical simulations. We define and evaluate several effective mass terms corresponding to the Euler equations of gas dynamics, and quantify the degree of the validity of HSE in terms of the mass estimate. We find that the mass estimated under the HSE assumption (the HSE mass) deviates from the true mass by up to {approx}30%. This level of departure from HSE is consistent with the previous claims, but our physical interpretation is rather different. We demonstrate that the inertial term inmore » the Euler equations makes a negligible contribution to the total mass, and the overall gravity of the cluster is balanced by the thermal gas pressure gradient and the gas acceleration term. Indeed, the deviation from the HSE mass is well explained by the acceleration term at almost all radii. We also clarify the confusion of previous work due to the inappropriate application of the Jeans equations in considering the validity of HSE from the gas dynamics extracted from cosmological hydrodynamical simulations.« less

Molecular definition of red cell Rh haplotypes by tightly linked SphI RFLPs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, C.H.; Reid, M.E.; Chen, Y.

The Rh blood group system of human red cells contains five major antigens D, C/c, and E/e (the latter four designated {open_quotes}non-D{close_quotes}) that are specified by eight gene complexes known as Rh haplotypes. In this paper, we report on the mapping of the RH locus and identification of a set of SphI RFLPs that are tightly linked with the Rh structural genes. Using exon-specific probes, we have localized the SphI cleavage sites resulting in these DNA markers and derived a comprehensive map for the RH locus. It was found that the SphI fragments encompassing exons 4-7 of the Rh genesmore » occur in four banding patterns or frameworks that correspond to the distribution and segregation of the common Rh haplotypes. This linkage disequilibrium allowed a genotype-phenotype correlation and direct determination of Rh zygosity related to the Rh-positive or Rh-negative status (D/D, D/d, and d/d). Studies on the occurrence of SphI RFLPs in a number of rare Rh variants indicated that Rh phenotypic diversity has taken place on different haplotype backgrounds and has arisen by diverse genetic mechanisms. The molecular definition of Rh haplotypes by SphI RFLP frameworks should provide a useful procedure for genetic counseling and prenatal assessment of Rh alloimmunization. 32 refs., 7 figs., 3 tabs.« less

Quercetin ameliorates pulmonary fibrosis by inhibiting SphK1/S1P signaling.

PubMed

Zhang, Xingcai; Cai, Yuli; Zhang, Wei; Chen, Xianhai

2018-06-25

Idiopathic pulmonary fibrosis (IPF) is an agnogenic chronic disorder with high morbidity and low survival rate. Quercetin is a flavonoid found in a variety of herbs with anti-fibrosis function. In this study, bleomycin was employed to induce a pulmonary fibrosis mouse model. The quercetin administration ameliorated bleomycin-induced pulmonary fibrosis, evidenced by the expression level changes of hydroxyproline, fibronectin, α-smooth muscle actin, Collagen I and Collagen III. The similar results were observed in transforming growth factor (TGF)-β-treated human embryonic lung fibroblast (HELF). The bleomycin or TGF-β administration caused the increase of sphingosine-1-phosphate (S1P) level in pulmonary tissue and HELF cells, as well as its activation-required kinase, sphingosine kinase 1 (SphK1), and its degradation enzyme, sphinogosine-1-phosphate lyase (S1PL). However, the increase of S1P, SphK1 and S1PL was attenuated by application of quercetin. In addition, the effect of quercetin on fibrosis was abolished by the ectopic expression of SphK1. The colocalization of SphK1/S1PL and fibroblast specific protein 1 (FSP1) suggested the roles of fibroblasts in pulmonary fibrosis. In summary, we demonstrated that quercetin ameliorated pulmonary fibrosis in vivo and in vitro by inhibiting SphK1/S1P signaling.

Hydrodynamic escape from planetary atmospheres

NASA Astrophysics Data System (ADS)

Tian, Feng

Hydrodynamic escape is an important process in the formation and evolution of planetary atmospheres. Due to the existence of a singularity point near the transonic point, it is difficult to find transonic steady state solutions by solving the time-independent hydrodynamic equations. In addition to that, most previous works assume that all energy driving the escape flow is deposited in one narrow layer. This assumption not only results in less accurate solutions to the hydrodynamic escape problem, but also makes it difficult to include other chemical and physical processes in the hydrodynamic escape models. In this work, a numerical model describing the transonic hydrodynamic escape from planetary atmospheres is developed. A robust solution technique is used to solve the time dependent hydrodynamic equations. The method has been validated in an isothermal atmosphere where an analytical solution is available. The hydrodynamic model is applied to 3 cases: hydrogen escape from small orbit extrasolar planets, hydrogen escape from a hydrogen rich early Earth's atmosphere, and nitrogen/methane escape from Pluto's atmosphere. Results of simulations on extrasolar planets are in good agreement with the observations of the transiting extrasolar planet HD209458b. Hydrodynamic escape of hydrogen from other hypothetical close-in extrasolar planets are simulated and the influence of hydrogen escape on the long-term evolution of these extrasolar planets are discussed. Simulations on early Earth suggest that hydrodynamic escape of hydrogen from a hydrogen rich early Earth's atmosphere is about two orders magnitude slower than the diffusion limited escape rate. A hydrogen rich early Earth's atmosphere could have been maintained by the balance between the hydrogen escape and the supply of hydrogen into the atmosphere by volcanic outgassing. Origin of life may have occurred in the organic soup ocean created by the efficient formation of prebiotic molecules in the hydrogen rich early

Small-body deflection techniques using spacecraft: Techniques in simulating the fate of ejecta

NASA Astrophysics Data System (ADS)

Schwartz, Stephen R.; Yu, Yang; Michel, Patrick; Jutzi, Martin

2016-04-01

We define a set of procedures to numerically study the fate of ejecta produced by the impact of an artificial projectile with the aim of deflecting an asteroid. Here we develop a simplified, idealized model of impact conditions that can be adapted to fit the details of specific deflection-test scenarios, such as what is being proposed for the AIDA project. Ongoing studies based upon the methodology described here can be used to inform observational strategies and safety conditions for an observing spacecraft. To account for ejecta evolution, the numerical strategies we are employing are varied and include a large N-Body component, a smoothed-particle hydrodynamics (SPH) component, and an application of impactor scaling laws. Simulations that use SPH-derived initial conditions show high-speed ejecta escaping at low angles of inclination, and very slowly moving ejecta lofting off the surface at higher inclination angles, some of which reimpacts the small-body surface. We are currently investigating the realism of this and other models' behaviors. Next steps will include the addition of solar perturbations to the model and applying the protocol developed here directly to specific potential mission concepts such as the proposed AIDA scenario.

Intercomparison of 3D pore-scale flow and solute transport simulation methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xiaofan; Mehmani, Yashar; Perkins, William A.

2016-09-01

Multiple numerical approaches have been developed to simulate porous media fluid flow and solute transport at the pore scale. These include methods that 1) explicitly model the three-dimensional geometry of pore spaces and 2) those that conceptualize the pore space as a topologically consistent set of stylized pore bodies and pore throats. In previous work we validated a model of class 1, based on direct numerical simulation using computational fluid dynamics (CFD) codes, against magnetic resonance velocimetry (MRV) measurements of pore-scale velocities. Here we expand that validation to include additional models of class 1 based on the immersed-boundary method (IMB),more » lattice Boltzmann method (LBM), smoothed particle hydrodynamics (SPH), as well as a model of class 2 (a pore-network model or PNM). The PNM approach used in the current study was recently improved and demonstrated to accurately simulate solute transport in a two-dimensional experiment. While the PNM approach is computationally much less demanding than direct numerical simulation methods, the effect of conceptualizing complex three-dimensional pore geometries on solute transport in the manner of PNMs has not been fully determined. We apply all four approaches (CFD, LBM, SPH and PNM) to simulate pore-scale velocity distributions and nonreactive solute transport, and intercompare the model results with previously reported experimental observations. Experimental observations are limited to measured pore-scale velocities, so solute transport comparisons are made only among the various models. Comparisons are drawn both in terms of macroscopic variables (e.g., permeability, solute breakthrough curves) and microscopic variables (e.g., local velocities and concentrations).« less

SPH Simulations of Spherical Bondi Accretion: First Step of Implementing AGN Feedback in Galaxy Formation

NASA Astrophysics Data System (ADS)

Barai, Paramita; Proga, D.; Nagamine, K.

2011-01-01

Our motivation is to numerically test the assumption of Black Hole (BH) accretion (that the central massive BH of a galaxy accretes mass at the Bondi-Hoyle accretion rate, with ad-hoc choice of parameters), made in many previous galaxy formation studies including AGN feedback. We perform simulations of a spherical distribution of gas, within the radius range 0.1 - 200 pc, accreting onto a central supermassive black hole (the Bondi problem), using the 3D Smoothed Particle Hydrodynamics code Gadget. In our simulations we study the radial distribution of various gas properties (density, velocity, temperature, Mach number). We compute the central mass inflow rate at the inner boundary (0.1 pc), and investigate how different gas properties (initial density and velocity profiles) and computational parameters (simulation outer boundary, particle number) affect the central inflow. Radiative processes (namely heating by a central X-ray corona and gas cooling) have been included in our simulations. We study the thermal history of accreting gas, and identify the contribution of radiative and adiabatic terms in shaping the gas properties. We find that the current implementation of artificial viscosity in the Gadget code causes unwanted extra heating near the inner radius.

Molecular mechanism for sphingosine-induced Pseudomonas ceramidase expression through the transcriptional regulator SphR

PubMed Central

Okino, Nozomu; Ito, Makoto

2016-01-01

Pseudomonas aeruginosa, an opportunistic, but serious multidrug-resistant pathogen, secretes a ceramidase capable of cleaving the N-acyl linkage of ceramide to generate fatty acids and sphingosine. We previously reported that the secretion of P. aeruginosa ceramidase was induced by host-derived sphingolipids, through which phospholipase C-induced hemolysis was significantly enhanced. We herein investigated the gene(s) regulating sphingolipid-induced ceramidase expression and identified SphR, which encodes a putative AraC family transcriptional regulator. Disruption of the sphR gene in P. aeruginosa markedly decreased the sphingomyelin-induced secretion of ceramidase, reduced hemolytic activity, and resulted in the loss of sphingomyelin-induced ceramidase expression. A microarray analysis confirmed that sphingomyelin significantly induced ceramidase expression in P. aeruginosa. Furthermore, an electrophoretic mobility shift assay revealed that SphR specifically bound free sphingoid bases such as sphingosine, dihydrosphingosine, and phytosphingosine, but not sphingomyelin or ceramide. A β-galactosidase-assisted promoter assay showed that sphingosine activated ceramidase expression through SphR at a concentration of 100 nM. Collectively, these results demonstrated that sphingosine induces the secretion of ceramidase by promoting the mRNA expression of ceramidase through SphR, thereby enhancing hemolytic phospholipase C-induced cytotoxicity. These results facilitate understanding of the physiological role of bacterial ceramidase in host cells. PMID:27941831

Production code control system for hydrodynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Slone, D.M.

1997-08-18

We describe how the Production Code Control System (pCCS), written in Perl, has been used to control and monitor the execution of a large hydrodynamics simulation code in a production environment. We have been able to integrate new, disparate, and often independent, applications into the PCCS framework without the need to modify any of our existing application codes. Both users and code developers see a consistent interface to the simulation code and associated applications regardless of the physical platform, whether an MPP, SMP, server, or desktop workstation. We will also describe our use of Perl to develop a configuration managementmore » system for the simulation code, as well as a code usage database and report generator. We used Perl to write a backplane that allows us plug in preprocessors, the hydrocode, postprocessors, visualization tools, persistent storage requests, and other codes. We need only teach PCCS a minimal amount about any new tool or code to essentially plug it in and make it usable to the hydrocode. PCCS has made it easier to link together disparate codes, since using Perl has removed the need to learn the idiosyncrasies of system or RPC programming. The text handling in Perl makes it easy to teach PCCS about new codes, or changes to existing codes.« less

Evaluation of superporous hydrogel (SPH) and SPH composite in porcine intestine ex-vivo: assessment of drug transport, morphology effect, and mechanical fixation to intestinal wall.

PubMed

Dorkoosh, Farid A; Borchard, Gerrit; Rafiee-Tehrani, Morteza; Verhoef, J Coos; Junginger, Hans E

2002-03-01

The objective of this study was to investigate the potential of superporous hydrogel (SPH) and SPH composite (SPHC) polymers to enhance the transport of N-alpha-benzoyl-L-arginine ethylester (BAEE) and fluorescein isothiocyanate-dextran 4400 (FD4) across porcine intestinal epithelium ex-vivo, and to study any possible morphological damage to the epithelium by applying these polymers. In addition, the ability of these polymers to attach to the gut wall by mechanical pressure was examined by using a specifically designed centrifuge model. The transport of BAEE and FD4 across the intestinal mucosa was enhanced 2- to 3-fold by applying SPHC polymer in comparison to negative control. No significant morphological damage was observed by applying these polymers inside the intestinal lumen. Moreover, the SPH and SPHC polymers were able to attach mechanically to the intestinal wall by swelling and did not move in the intestinal lumen even when a horizontal force of 13 gms(-2) was applied. In conclusion, these polymers are appropriate vehicles for enhancing the intestinal absorption of peptide and protein drugs.

Thermally robust Au99(SPh)42 nanoclusters for chemoselective hydrogenation of nitrobenzaldehyde derivatives in water.

PubMed

Li, Gao; Zeng, Chenjie; Jin, Rongchao

2014-03-05

We report the synthesis and catalytic application of thermally robust gold nanoclusters formulated as Au99(SPh)42. The formula was determined by electrospray ionization and matrix-assisted laser desorption ionization mass spectrometry in conjunction with thermogravimetric analysis. The optical spectrum of Au99(SPh)42 nanoclusters shows absorption peaks at ~920 nm (1.35 eV), 730 nm (1.70 eV), 600 nm (2.07 eV), 490 nm (2.53 eV), and 400 nm (3.1 eV) in contrast to conventional gold nanoparticles, which exhibit a plasmon resonance band at 520 nm (for spherical particles). The ceria-supported Au99(SPh)42 nanoclusters were utilized as a catalyst for chemoselective hydrogenation of nitrobenzaldehyde to nitrobenzyl alcohol in water using H2 gas as the hydrogen source. The selective hydrogenation of the aldehyde group catalyzed by nanoclusters is a surprise because conventional nanogold catalysts instead give rise to the product resulting from reduction of the nitro group. The Au99(SPh)42/CeO2 catalyst gives high catalytic activity for a range of nitrobenzaldehyde derivatives and also shows excellent recyclability due to its thermal robustness. We further tested the size-dependent catalytic performance of Au25(SPh)18 and Au36(SPh)24 nanoclusters, and on the basis of their crystal structures we propose a molecular adsorption site for nitrobenzaldehyde. The nanocluster material is expected to find wide application in catalytic reactions.

Identification of a novel SPLIT-HULL (SPH) gene associated with hull splitting in rice (Oryza sativa L.).

PubMed

Lee, Gileung; Lee, Kang-Ie; Lee, Yunjoo; Kim, Backki; Lee, Dongryung; Seo, Jeonghwan; Jang, Su; Chin, Joong Hyoun; Koh, Hee-Jong

2018-07-01

The split-hull phenotype caused by reduced lemma width and low lignin content is under control of SPH encoding a type-2 13-lipoxygenase and contributes to high dehulling efficiency. Rice hulls consist of two bract-like structures, the lemma and palea. The hull is an important organ that helps to protect seeds from environmental stress, determines seed shape, and ensures grain filling. Achieving optimal hull size and morphology is beneficial for seed development. We characterized the split-hull (sph) mutant in rice, which exhibits hull splitting in the interlocking part between lemma and palea and/or the folded part of the lemma during the grain filling stage. Morphological and chemical analysis revealed that reduction in the width of the lemma and lignin content of the hull in the sph mutant might be the cause of hull splitting. Genetic analysis indicated that the mutant phenotype was controlled by a single recessive gene, sph (Os04g0447100), which encodes a type-2 13-lipoxygenase. SPH knockout and knockdown transgenic plants displayed the same split-hull phenotype as in the mutant. The sph mutant showed significantly higher linoleic and linolenic acid (substrates of lipoxygenase) contents in spikelets compared to the wild type. It is probably due to the genetic defect of SPH and subsequent decrease in lipoxygenase activity. In dehulling experiment, the sph mutant showed high dehulling efficiency even by a weak tearing force in a dehulling machine. Collectively, the results provide a basis for understanding of the functional role of lipoxygenase in structure and maintenance of hulls, and would facilitate breeding of easy-dehulling rice.

Local Group dSph radio survey with ATCA (III): constraints on particle dark matter

NASA Astrophysics Data System (ADS)

Regis, Marco; Colafrancesco, Sergio; Profumo, Stefano; de Blok, W. J. G.; Massardi, Marcella; Richter, Laura

2014-10-01

We performed a deep search for radio synchrotron emissions induced by weakly interacting massive particles (WIMPs) annihilation or decay in six dwarf spheroidal (dSph) galaxies of the Local Group. Observations were conducted with the Australia Telescope Compact Array (ATCA) at 16 cm wavelength, with an rms sensitivity better than 0.05 mJy/beam in each field. In this work, we first discuss the uncertainties associated with the modeling of the expected signal, such as the shape of the dark matter (DM) profile and the dSph magnetic properties. We then investigate the possibility that point-sources detected in the proximity of the dSph optical center might be due to the emission from a DM cuspy profile. No evidence for an extended emission over a size of few arcmin (which is the DM halo size) has been detected. We present the associated bounds on the WIMP parameter space for different annihilation/decay final states and for different astrophysical assumptions. If the confinement of electrons and positrons in the dSph is such that the majority of their power is radiated within the dSph region, we obtain constraints on the WIMP annihilation rate which are well below the thermal value for masses up to few TeV. On the other hand, for conservative assumptions on the dSph magnetic properties, the bounds can be dramatically relaxed. We show however that, within the next 10 years and regardless of the astrophysical assumptions, it will be possible to progressively close in on the full parameter space of WIMPs by searching for radio signals in dSphs with SKA and its precursors.

Shrimp serine proteinase homologues PmMasSPH-1 and -2 play a role in the activation of the prophenoloxidase system.

PubMed

Jearaphunt, Miti; Amparyup, Piti; Sangsuriya, Pakkakul; Charoensapsri, Walaiporn; Senapin, Saengchan; Tassanakajon, Anchalee

2015-01-01

Melanization mediated by the prophenoloxidase (proPO) activating system is a rapid immune response used by invertebrates against intruding pathogens. Several masquerade-like and serine proteinase homologues (SPHs) have been demonstrated to play an essential role in proPO activation in insects and crustaceans. In a previous study, we characterized the masquerade-like SPH, PmMasSPH1, in the black tiger shrimp Penaeus monodon as a multifunctional immune protein based on its recognition and antimicrobial activity against the Gram-negative bacteria Vibrio harveyi. In the present study, we identify a novel SPH, known as PmMasSPH2, composed of an N-terminal clip domain and a C-terminal SP-like domain that share high similarity to those of other insect and crustacean SPHs. We demonstrate that gene silencing of PmMasSPH1 and PmMasSPH2 significantly reduces PO activity, resulting in a high number of V. harveyi in the hemolymph. Interestingly, knockdown of PmMasSPH1 suppressed not only its gene transcript but also other immune-related genes in the proPO system (e.g., PmPPAE2) and antimicrobial peptides (e.g., PenmonPEN3, PenmonPEN5, crustinPm1 and Crus-likePm). The PmMasSPH1 and PmMasSPH2 also show binding activity to peptidoglycan (PGN) of Gram-positive bacteria. Using a yeast two-hybrid analysis and co-immunoprecipitation, we demonstrate that PmMasSPH1 specifically interacted with the final proteinase of the proPO cascade, PmPPAE2. Furthermore, the presence of both PmMasSPH1 and PmPPAE2 enhances PGN-induced PO activity in vitro. Taken together, these results suggest the importance of PmMasSPHs in the activation of the shrimp proPO system.

Shrimp Serine Proteinase Homologues PmMasSPH-1 and -2 Play a Role in the Activation of the Prophenoloxidase System

PubMed Central

Jearaphunt, Miti; Amparyup, Piti; Sangsuriya, Pakkakul; Charoensapsri, Walaiporn; Senapin, Saengchan; Tassanakajon, Anchalee

2015-01-01

Melanization mediated by the prophenoloxidase (proPO) activating system is a rapid immune response used by invertebrates against intruding pathogens. Several masquerade-like and serine proteinase homologues (SPHs) have been demonstrated to play an essential role in proPO activation in insects and crustaceans. In a previous study, we characterized the masquerade-like SPH, PmMasSPH1, in the black tiger shrimp Penaeus monodon as a multifunctional immune protein based on its recognition and antimicrobial activity against the Gram-negative bacteria Vibrio harveyi. In the present study, we identify a novel SPH, known as PmMasSPH2, composed of an N-terminal clip domain and a C-terminal SP-like domain that share high similarity to those of other insect and crustacean SPHs. We demonstrate that gene silencing of PmMasSPH1 and PmMasSPH2 significantly reduces PO activity, resulting in a high number of V. harveyi in the hemolymph. Interestingly, knockdown of PmMasSPH1 suppressed not only its gene transcript but also other immune-related genes in the proPO system (e.g., PmPPAE2) and antimicrobial peptides (e.g., PenmonPEN3, PenmonPEN5, crustinPm1 and Crus-likePm). The PmMasSPH1 and PmMasSPH2 also show binding activity to peptidoglycan (PGN) of Gram-positive bacteria. Using a yeast two-hybrid analysis and co-immunoprecipitation, we demonstrate that PmMasSPH1 specifically interacted with the final proteinase of the proPO cascade, PmPPAE2. Furthermore, the presence of both PmMasSPH1 and PmPPAE2 enhances PGN-induced PO activity in vitro. Taken together, these results suggest the importance of PmMasSPHs in the activation of the shrimp proPO system. PMID:25803442

The SELGIFS data challenge: generating synthetic observations of CALIFA galaxies from hydrodynamical simulations

NASA Astrophysics Data System (ADS)

Guidi, G.; Casado, J.; Ascasibar, Y.; García-Benito, R.; Galbany, L.; Sánchez-Blázquez, P.; Sánchez, S. F.; Rosales-Ortega, F. F.; Scannapieco, C.

2018-06-01

In this work we present a set of synthetic observations that mimic the properties of the Integral Field Spectroscopy (IFS) survey CALIFA, generated using radiative transfer techniques applied to hydrodynamical simulations of galaxies in a cosmological context. The simulated spatially-resolved spectra include stellar and nebular emission, kinematic broadening of the lines, and dust extinction and scattering. The results of the radiative transfer simulations have been post-processed to reproduce the main properties of the CALIFA V500 and V1200 observational setups. The data has been further formatted to mimic the CALIFA survey in terms of field of view size, spectral range and sampling. We have included the effect of the spatial and spectral Point Spread Functions affecting CALIFA observations, and added detector noise after characterizing it on a sample of 367 galaxies. The simulated datacubes are suited to be analysed by the same algorithms used on real IFS data. In order to provide a benchmark to compare the results obtained applying IFS observational techniques to our synthetic datacubes, and test the calibration and accuracy of the analysis tools, we have computed the spatially-resolved properties of the simulations. Hence, we provide maps derived directly from the hydrodynamical snapshots or the noiseless spectra, in a way that is consistent with the values recovered by the observational analysis algorithms. Both the synthetic observations and the product datacubes are public and can be found in the collaboration website http://astro.ft.uam.es/selgifs/data_challenge/.

Transformation of Au144(SCH2CH2Ph)60 to Au133(SPh-tBu)52 Nanomolecules: Theoretical and Experimental Study.

PubMed

Nimmala, Praneeth Reddy; Theivendran, Shevanuja; Barcaro, Giovanni; Sementa, Luca; Kumara, Chanaka; Jupally, Vijay Reddy; Apra, Edoardo; Stener, Mauro; Fortunelli, Alessandro; Dass, Amala

2015-06-04

Ultrastable gold nanomolecule Au144(SCH2CH2Ph)60 upon etching with excess tert-butylbenzenethiol undergoes a core-size conversion and compositional change to form an entirely new core of Au133(SPh-tBu)52. This conversion was studied using high-resolution electrospray mass spectrometry which shows that the core size conversion is initiated after 22 ligand exchanges, suggesting a relatively high stability of the Au144(SCH2CH2Ph)38(SPh-tBu)22 intermediate. The Au144 → Au133 core size conversion is surprisingly different from the Au144 → Au99 core conversion reported in the case of thiophenol, -SPh. Theoretical analysis and ab initio molecular dynamics simulations show that rigid p-tBu groups play a crucial role by reducing the cluster structural freedom, and protecting the cluster from adsorption of exogenous and reactive species, thus rationalizing the kinetic factors that stabilize the Au133 core size. This 144-atom to 133-atom nanomolecule's compositional change is reflected in optical spectroscopy and electrochemistry.

3D Hydrodynamic Simulation of Classical Novae Explosions

NASA Astrophysics Data System (ADS)

Kendrick, Coleman J.

2015-01-01

This project investigates the formation and lifecycle of classical novae and determines how parameters such as: white dwarf mass, star mass and separation affect the evolution of the rotating binary system. These parameters affect the accretion rate, frequency of the nova explosions and light curves. Each particle in the simulation represents a volume of hydrogen gas and are initialized randomly in the outer shell of the companion star. The forces on each particle include: gravity, centrifugal, coriolis, friction, and Langevin. The friction and Langevin forces are used to model the viscosity and internal pressure of the gas. A velocity Verlet method with a one second time step is used to compute velocities and positions of the particles. A new particle recycling method was developed which was critical for computing an accurate and stable accretion rate and keeping the particle count reasonable. I used C++ and OpenCL to create my simulations and ran them on two Nvidia GTX580s. My simulations used up to 1 million particles and required up to 10 hours to complete. My simulation results for novae U Scorpii and DD Circinus are consistent with professional hydrodynamic simulations and observed experimental data (light curves and outburst frequencies). When the white dwarf mass is increased, the time between explosions decreases dramatically. My model was used to make the first prediction for the next outburst of nova DD Circinus. My simulations also show that the companion star blocks the expanding gas shell leading to an asymmetrical expanding shell.

Steady-state hydrodynamic instabilities of active liquid crystals: hybrid lattice Boltzmann simulations.

PubMed

Marenduzzo, D; Orlandini, E; Cates, M E; Yeomans, J M

2007-09-01

We report hybrid lattice Boltzmann (HLB) simulations of the hydrodynamics of an active nematic liquid crystal sandwiched between confining walls with various anchoring conditions. We confirm the existence of a transition between a passive phase and an active phase, in which there is spontaneous flow in the steady state. This transition is attained for sufficiently "extensile" rods, in the case of flow-aligning liquid crystals, and for sufficiently "contractile" ones for flow-tumbling materials. In a quasi-one-dimensional geometry, deep in the active phase of flow-aligning materials, our simulations give evidence of hysteresis and history-dependent steady states, as well as of spontaneous banded flow. Flow-tumbling materials, in contrast, rearrange themselves so that only the two boundary layers flow in steady state. Two-dimensional simulations, with periodic boundary conditions, show additional instabilities, with the spontaneous flow appearing as patterns made up of "convection rolls." These results demonstrate a remarkable richness (including dependence on anchoring conditions) in the steady-state phase behavior of active materials, even in the absence of external forcing; they have no counterpart for passive nematics. Our HLB methodology, which combines lattice Boltzmann for momentum transport with a finite difference scheme for the order parameter dynamics, offers a robust and efficient method for probing the complex hydrodynamic behavior of active nematics.

Numerical Hydrodynamics in General Relativity.

PubMed

Font, José A

2003-01-01

The current status of numerical solutions for the equations of ideal general relativistic hydrodynamics is reviewed. With respect to an earlier version of the article, the present update provides additional information on numerical schemes, and extends the discussion of astrophysical simulations in general relativistic hydrodynamics. Different formulations of the equations are presented, with special mention of conservative and hyperbolic formulations well-adapted to advanced numerical methods. A large sample of available numerical schemes is discussed, paying particular attention to solution procedures based on schemes exploiting the characteristic structure of the equations through linearized Riemann solvers. A comprehensive summary of astrophysical simulations in strong gravitational fields is presented. These include gravitational collapse, accretion onto black holes, and hydrodynamical evolutions of neutron stars. The material contained in these sections highlights the numerical challenges of various representative simulations. It also follows, to some extent, the chronological development of the field, concerning advances on the formulation of the gravitational field and hydrodynamic equations and the numerical methodology designed to solve them. Supplementary material is available for this article at 10.12942/lrr-2003-4.

Hydrodynamic interactions in active colloidal crystal microrheology.

PubMed

Weeber, R; Harting, J

2012-11-01

In dense colloids it is commonly assumed that hydrodynamic interactions do not play a role. However, a found theoretical quantification is often missing. We present computer simulations that are motivated by experiments where a large colloidal particle is dragged through a colloidal crystal. To qualify the influence of long-ranged hydrodynamics, we model the setup by conventional Langevin dynamics simulations and by an improved scheme with limited hydrodynamic interactions. This scheme significantly improves our results and allows to show that hydrodynamics strongly impacts the development of defects, the crystal regeneration, as well as the jamming behavior.

The magnetic universe through vector potential SPMHD simulations

NASA Astrophysics Data System (ADS)

Stasyszyn, F. A.

2017-10-01

The use of Smoothed Particle Magneto Hydrodynamics (SPMHD) is getting nowadays more and more common in Astrophysics. From galaxy clusters to neutron starts, there are multiple applications already existing in the literature. I will review some of the common methods used and highlight the successful approach of using vector potentials to describe the evolution of the magnetic fields. The latter have some interesting advantages, and their results challenge previous findings, being the magnetic divergence problem naturally vanished. We select a few examples to discuss some areas of interest. First, we show some Galaxy Clusters from the MUSIC project. These cosmological simulations are done with the usual sub-grid recipes, as radiative cooling and star formation, being the first ones obtained with an SPH code in a self consistent way. This demonstrates the robustness of the new method in a variety of astrophysical scenarios.

Does Explosive Nuclear Burning Occur in Tidal Disruption Events of White Dwarfs by Intermediate-mass Black Holes?

NASA Astrophysics Data System (ADS)

Tanikawa, Ataru; Sato, Yushi; Nomoto, Ken'ichi; Maeda, Keiichi; Nakasato, Naohito; Hachisu, Izumi

2017-04-01

We investigate nucleosynthesis in tidal disruption events (TDEs) of white dwarfs (WDs) by intermediate-mass black holes. We consider various types of WDs with different masses and compositions by means of three-dimensional (3D) smoothed particle hydrodynamics (SPH) simulations. We model these WDs with different numbers of SPH particles, N, from a few 104 to a few 107 in order to check mass resolution convergence, where SPH simulations with N > 107 (or a space resolution of several 106 cm) have unprecedentedly high resolution in this kind of simulation. We find that nuclear reactions become less active with increasing N and that these nuclear reactions are excited by spurious heating due to low resolution. Moreover, we find no shock wave generation. In order to investigate the reason for the absence of a shock wave, we additionally perform one-dimensional (1D) SPH and mesh-based simulations with a space resolution ranging from 104 to 107 cm, using a characteristic flow structure extracted from the 3D SPH simulations. We find shock waves in these 1D high-resolution simulations, one of which triggers a detonation wave. However, we must be careful of the fact that, if the shock wave emerged in an outer region, it could not trigger the detonation wave due to low density. Note that the 1D initial conditions lack accuracy to precisely determine where a shock wave emerges. We need to perform 3D simulations with ≲106 cm space resolution in order to conclude that WD TDEs become optical transients powered by radioactive nuclei.

Fully Implict Magneto-hydrodynamics Simulations of Coaxial Plasma Accelerators

DOE PAGES

Subramaniam, Vivek; Raja, Laxminarayan L.

2017-01-05

The resistive Magneto-Hydrodynamic (MHD) model describes the behavior of a strongly ionized plasma in the presence of external electric and magnetic fields. We developed a fully implicit MHD simulation tool to solve the resistive MHD governing equations in the context of a cell-centered finite-volume scheme. The primary objective of this study is to use the fully-implicit algorithm to obtain insights into the plasma acceleration and jet formation processes in Coaxial Plasma accelerators; electromagnetic acceleration devices that utilize self-induced magnetic fields to accelerate thermal plasmas to large velocities. We also carry out plasma-surface simulations in order to study the impact interactionsmore » when these high velocity plasma jets impinge on target material surfaces. Scaling studies are carried out to establish some basic functional relationships between the target-stagnation conditions and the current discharged between the coaxial electrodes.« less

Local Group dSph radio survey with ATCA - II. Non-thermal diffuse emission

NASA Astrophysics Data System (ADS)

Regis, Marco; Richter, Laura; Colafrancesco, Sergio; Profumo, Stefano; de Blok, W. J. G.; Massardi, Marcella

2015-04-01

Our closest neighbours, the Local Group dwarf spheroidal (dSph) galaxies, are extremely quiescent and dim objects, where thermal and non-thermal diffuse emissions lack, so far, of detection. In order to possibly study the dSph interstellar medium, deep observations are required. They could reveal non-thermal emissions associated with the very low level of star formation, or to particle dark matter annihilating or decaying in the dSph halo. In this work, we employ radio observations of six dSphs, conducted with the Australia Telescope Compact Array in the frequency band 1.1-3.1 GHz, to test the presence of a diffuse component over typical scales of few arcmin and at an rms sensitivity below 0.05 mJy beam-1. We observed the dSph fields with both a compact array and long baselines. Short spacings led to a synthesized beam of about 1 arcmin and were used for the extended emission search. The high-resolution data mapped background sources, which in turn were subtracted in the short-baseline maps, to reduce their confusion limit. We found no significant detection of a diffuse radio continuum component. After a detailed discussion on the modelling of the cosmic ray (CR) electron distribution and on the dSph magnetic properties, we present bounds on several physical quantities related to the dSphs, such that the total radio flux, the angular shape of the radio emissivity, the equipartition magnetic field, and the injection and equilibrium distributions of CR electrons. Finally, we discuss the connection to far-infrared and X-ray observations.

Numerical calculation of protein-ligand binding rates through solution of the Smoluchowski equation using smooth particle hydrodynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pan, Wenxiao; Daily, Michael D.; Baker, Nathan A.

2015-12-01

We demonstrate the accuracy and effectiveness of a Lagrangian particle-based method, smoothed particle hydrodynamics (SPH), to study diffusion in biomolecular systems by numerically solving the time-dependent Smoluchowski equation for continuum diffusion. The numerical method is first verified in simple systems and then applied to the calculation of ligand binding to an acetylcholinesterase monomer. Unlike previous studies, a reactive Robin boundary condition (BC), rather than the absolute absorbing (Dirichlet) boundary condition, is considered on the reactive boundaries. This new boundary condition treatment allows for the analysis of enzymes with "imperfect" reaction rates. Rates for inhibitor binding to mAChE are calculated atmore » various ionic strengths and compared with experiment and other numerical methods. We find that imposition of the Robin BC improves agreement between calculated and experimental reaction rates. Although this initial application focuses on a single monomer system, our new method provides a framework to explore broader applications of SPH in larger-scale biomolecular complexes by taking advantage of its Lagrangian particle-based nature.« less

Testing core creation in hydrodynamical simulations using the HI kinematics of field dwarfs

NASA Astrophysics Data System (ADS)

Papastergis, E.; Ponomareva, A. A.

2017-05-01

The majority of recent hydrodynamical simulations indicate the creation of central cores in the mass profiles of low-mass halos, a process that is attributed to star formation-related baryonic feedback. Core creation is regarded as one of the most promising solutions to potential issues faced by lambda cold dark matter (ΛCDM) cosmology on small scales. For example, the reduced dynamical mass enclosed by cores can explain the low rotational velocities measured for nearby dwarf galaxies, thus possibly lifting the seeming contradiction with the ΛCDM expectations (the so-called "too big to fail" problem). Here we test core creation as a solution of cosmological issues by using a sample of dwarfs with measurements of their atomic hydrogen (HI) kinematics extending to large radii. Using the NIHAO hydrodynamical simulation as an example, we show that core creation can successfully reproduce the kinematics of dwarfs with small kinematic radii, R ≲ 1.5 kpc. However, the agreement with observations becomes poor once galaxies with kinematic measurements extending beyond the core region, R ≈ 1.5-4 kpc, are considered. This result illustrates the importance of testing the predictions of hydrodynamical simulations that are relevant for cosmology against a broad range of observational samples. We would like to stress that our result is valid only under the following set of assumptions: I) that our sample of dwarfs with HI kinematics is representative of the overall population of field dwarfs; II) that there are no severe measurement biases in the observational parameters of our HI dwarfs (e.g., related to inclination estimates); and III) that the HI velocity fields of dwarfs are regular enough to allow the recovery of the true enclosed dynamical mass.

Mechanistic studies on the reactions of PhS(-) or [MoS(4)](2)(-) with [M(4)(SPh)(10)](2)(-) (M = Fe or Co).

PubMed

Cui, Zhen; Henderson, Richard A

2002-08-12

Kinetic studies, using stopped-flow spectrophotometry, on the reactions of [M(4)(SPh)(10)](2)(-) (M = Fe or Co) with PhS(-) to form [M(SPh)(4)](2)(-) are described, as are the reactions between [M(4)(SPh)(10)](2)(-) and [MoS(4)](2)(-) to form [S(2)MoS(2)Fe(SPh)(2)](2)(-) or [S(2)MoS(2)CoS(2)MoS(2)](2)(-). The kinetics of the reactions with PhS(-) are consistent with an initial associative substitution mechanism involving attack of PhS(-) at one of the tetrahedral M sites of [M(4)(SPh)(10)](2)(-) to form [M(4)(SPh)(11)](3)(-). Subsequent or concomitant cleavage of a micro-SPh ligand, at the same M, initiates a cascade of rapid reactions which result ultimately in the complete rupture of the cluster and formation of [M(SPh)(4)](2)(-). The kinetics of the reaction between [M(4)(SPh)(10)](2)(-) and [MoS(4)](2)(-) indicate an initial dissociative substitution mechanism at low concentrations of [MoS(4)](2)(-), in which rate-limiting dissociation of a terminal thiolate from [M(4)(SPh)(10)](2)(-) produces [M(4)(SPh)(9)](-) and the coordinatively unsaturated M site is rapidly attacked by a sulfido group of [MoS(4)](2)(-). It is proposed that subsequent chelation of the MoS(4) ligand results in cleavage of an M-micro-SPh bond, initiating a cascade of reactions which lead to the ultimate break-up of the cluster and formation of the products, [S(2)MoS(2)Fe(SPh)(2)](2)(-) or [S(2)MoS(2)CoS(2)MoS(2)](2)(-). With [Co(4)(SPh)(10)](2)(-), at higher concentrations of [MoS(4)](2)(-), a further substitution pathway is evident which exhibits a second order dependence on the concentration of [MoS(4)](2)(-). The mechanistic picture of cluster disruption which emerges from these studies rationalizes the "all or nothing" reactivity of [M(4)(SPh)(10)](2)(-).

Direct numerical simulation of stochastically forced laminar plane couette flow: peculiarities of hydrodynamic fluctuations.

PubMed

Khujadze, G; Oberlack, M; Chagelishvili, G

2006-07-21

The background of three-dimensional hydrodynamic (vortical) fluctuations in a stochastically forced, laminar, incompressible, plane Couette flow is simulated numerically. The fluctuating field is anisotropic and has well pronounced peculiarities: (i) the hydrodynamic fluctuations exhibit nonexponential, transient growth; (ii) fluctuations with the streamwise characteristic length scale about 2 times larger than the channel width are predominant in the fluctuating spectrum instead of streamwise constant ones; (iii) nonzero cross correlations of velocity (even streamwise-spanwise) components appear; (iv) stochastic forcing destroys the spanwise reflection symmetry (inherent to the linear and full Navier-Stokes equations in a case of the Couette flow) and causes an asymmetry of the dynamical processes.

Hydrodynamical simulations of the stream-core interaction in the slow merger of massive stars

NASA Astrophysics Data System (ADS)

Ivanova, N.; Podsiadlowski, Ph.; Spruit, H.

2002-08-01

We present detailed simulations of the interaction of a stream emanating from a mass-losing secondary with the core of a massive supergiant in the slow merger of two stars inside a common envelope. The dynamics of the stream can be divided into a ballistic phase, starting at the L1 point, and a hydrodynamical phase, where the stream interacts strongly with the core. Considering the merger of a 1- and 5-Msolar star with a 20-Msolar evolved supergiant, we present two-dimensional hydrodynamical simulations using the PROMETHEUS code to demonstrate how the penetration depth and post-impact conditions depend on the initial properties of the stream material (e.g. entropy, angular momentum, stream width) and the properties of the core (e.g. density structure and rotation rate). Using these results, we present a fitting formula for the entropy generated in the stream-core interaction and a recipe for the determination of the penetration depth based on a modified Bernoulli integral.

Particle Based Simulations of Complex Systems with MP2C : Hydrodynamics and Electrostatics

NASA Astrophysics Data System (ADS)

Sutmann, Godehard; Westphal, Lidia; Bolten, Matthias

2010-09-01

Particle based simulation methods are well established paths to explore system behavior on microscopic to mesoscopic time and length scales. With the development of new computer architectures it becomes more and more important to concentrate on local algorithms which do not need global data transfer or reorganisation of large arrays of data across processors. This requirement strongly addresses long-range interactions in particle systems, i.e. mainly hydrodynamic and electrostatic contributions. In this article, emphasis is given to the implementation and parallelization of the Multi-Particle Collision Dynamics method for hydrodynamic contributions and a splitting scheme based on Multigrid for electrostatic contributions. Implementations are done for massively parallel architectures and are demonstrated for the IBM Blue Gene/P architecture Jugene in Jülich.

Modelling large floating bodies in urban area flash-floods via a Smoothed Particle Hydrodynamics model

NASA Astrophysics Data System (ADS)

Albano, Raffaele; Sole, Aurelia; Mirauda, Domenica; Adamowski, Jan

2016-10-01

Large debris, including vehicles parked along floodplains, can cause severe damage and significant loss of life during urban area flash-floods. In this study, the authors validated and applied the Smoothed Particle Hydrodynamics (SPH) model, developed in Amicarelli et al. (2015), which reproduces in 3D the dynamics of rigid bodies driven by free surface flows, to the design of flood mitigation measures. To validate the model, the authors compared the model's predictions to the results of an experimental setup, involving a dam breach that strikes two fixed obstacles and three transportable floating bodies. Given the accuracy of the results, in terms of water depth over time and the time history of the bodies' movements, the SPH model explored in this study was used to analyse the mitigation efficiency of a proposed structural intervention - the use of small barriers (groynes) to prevent the transport of floating bodies. Different groynes configurations were examined to identify the most appropriate design and layout for urban area flash-flood damage mitigation. The authors found that groynes positioned upstream and downstream of each floating body can be effective as a risk mitigation measure for damage resulting from their movement.

Integral approximations to classical diffusion and smoothed particle hydrodynamics

DOE PAGES

Du, Qiang; Lehoucq, R. B.; Tartakovsky, A. M.

2014-12-31

The contribution of the paper is the approximation of a classical diffusion operator by an integral equation with a volume constraint. A particular focus is on classical diffusion problems associated with Neumann boundary conditions. By exploiting this approximation, we can also approximate other quantities such as the flux out of a domain. Our analysis of the model equation on the continuum level is closely related to the recent work on nonlocal diffusion and peridynamic mechanics. In particular, we elucidate the role of a volumetric constraint as an approximation to a classical Neumann boundary condition in the presence of physical boundary.more » The volume-constrained integral equation then provides the basis for accurate and robust discretization methods. As a result, an immediate application is to the understanding and improvement of the Smoothed Particle Hydrodynamics (SPH) method.« less

The effects of pressure dependent constitutive model to simulate concrete structures failure under impact loads

NASA Astrophysics Data System (ADS)

Mokhatar, S. N.; Sonoda, Y.; Kamarudin, A. F.; Noh, M. S. Md; Tokumaru, S.

2018-04-01

The main objective of this paper is to explore the effect of confining pressure in the compression and tension zone by simulating the behaviour of reinforced concrete/mortar structures subjected to the impact load. The analysis comprises the numerical simulation of the influences of high mass low speed impact weight dropping on concrete structures, where the analyses are incorporated with meshless method namely as Smoothed Particle Hydrodynamics (SPH) method. The derivation of the plastic stiffness matrix of Drucker-Prager (DP) that extended from Von-Mises (VM) yield criteria to simulate the concrete behaviour were presented in this paper. In which, the displacements for concrete/mortar structures are assumed to be infinitesimal. Furthermore, the influence of the different material model of DP and VM that used numerically for concrete and mortar structures are also discussed. Validation upon existing experimental test results is carried out to investigate the effect of confining pressure, it is found that VM criterion causes unreal impact failure (flexural cracking) of concrete structures.

Insulin-like growth factor binding protein-3 induces angiogenesis through IGF-I- and SphK1-dependent mechanisms.

PubMed

Granata, R; Trovato, L; Lupia, E; Sala, G; Settanni, F; Camussi, G; Ghidoni, R; Ghigo, E

2007-04-01

Angiogenesis is critical for development and repair, and is a prominent feature of many pathological conditions. Based on evidence that insulin-like growth factor binding protein (IGFBP)-3 enhances cell motility and activates sphingosine kinase (SphK) in human endothelial cells, we have investigated whether IGFBP-3 plays a role in promoting angiogenesis. IGFBP-3 potently induced network formation by human endothelial cells on Matrigel. Moreover, it up-regulated proangiogenic genes, such as vascular endothelial growth factor (VEGF) and matrix metalloproteinases (MMP)-2 and -9. IGFBP-3 even induced membrane-type 1 MMP (MT1-MMP), which regulates MMP-2 activation. Decreasing SphK1 expression by small interfering RNA (siRNA), blocked IGFBP-3-induced network formation and inhibited VEGF, MT1-MMP but not IGF-I up-regulation. IGF-I activated SphK, leading to sphingosine-1-phosphate (S1P) formation. The IGF-I effect on SphK activity was blocked by specific inhibitors of IGF-IR, PI3K/Akt and ERK1/2 phosphorylation. The disruption of IGF-I signaling prevented the IGFBP-3 effect on tube formation, SphK activity and VEGF release. Blocking ERK1/2 signaling caused the loss of SphK activation and VEGF and IGF-I up-regulation. Finally, IGFBP-3 dose-dependently stimulated neovessel formation into subcutaneous implants of Matrigel in vivo. Thus, IGFBP-3 positively regulates angiogenesis through involvement of IGF-IR signaling and subsequent SphK/S1P activation.

Frequency-dependent hydrodynamic interaction between two solid spheres

NASA Astrophysics Data System (ADS)

Jung, Gerhard; Schmid, Friederike

2017-12-01

Hydrodynamic interactions play an important role in many areas of soft matter science. In simulations with implicit solvent, various techniques such as Brownian or Stokesian dynamics explicitly include hydrodynamic interactions a posteriori by using hydrodynamic diffusion tensors derived from the Stokes equation. However, this equation assumes the interaction to be instantaneous which is an idealized approximation and only valid on long time scales. In the present paper, we go one step further and analyze the time-dependence of hydrodynamic interactions between finite-sized particles in a compressible fluid on the basis of the linearized Navier-Stokes equation. The theoretical results show that at high frequencies, the compressibility of the fluid has a significant impact on the frequency-dependent pair interactions. The predictions of hydrodynamic theory are compared to molecular dynamics simulations of two nanocolloids in a Lennard-Jones fluid. For this system, we reconstruct memory functions by extending the inverse Volterra technique. The simulation data agree very well with the theory, therefore, the theory can be used to implement dynamically consistent hydrodynamic interactions in the increasingly popular field of non-Markovian modeling.

Analysis of novel sph (spherocytosis) alleles in mice reveals allele-specific loss of band 3 and adducin in α-spectrin–deficient red cells

PubMed Central

Robledo, Raymond F.; Lambert, Amy J.; Birkenmeier, Connie S.; Cirlan, Marius V.; Cirlan, Andreea Flavia M.; Campagna, Dean R.; Lux, Samuel E.

2010-01-01

Five spontaneous, allelic mutations in the α-spectrin gene, Spna1, have been identified in mice (spherocytosis [sph], sph1J, sph2J, sph2BC, sphDem). All cause severe hemolytic anemia. Here, analysis of 3 new alleles reveals previously unknown consequences of red blood cell (RBC) spectrin deficiency. In sph3J, a missense mutation (H2012Y) in repeat 19 introduces a cryptic splice site resulting in premature termination of translation. In sphIhj, a premature stop codon occurs (Q1853Stop) in repeat 18. Both mutations result in markedly reduced RBC membrane spectrin content, decreased band 3, and absent β-adducin. Reevaluation of available, previously described sph alleles reveals band 3 and adducin deficiency as well. In sph4J, a missense mutation occurs in the C-terminal EF hand domain (C2384Y). Notably, an equally severe hemolytic anemia occurs despite minimally decreased membrane spectrin with normal band 3 levels and present, although reduced, β-adducin. The severity of anemia in sph4J indicates that the highly conserved cysteine residue at the C-terminus of α-spectrin participates in interactions critical to membrane stability. The data reinforce the notion that a membrane bridge in addition to the classic protein 4.1-p55-glycophorin C linkage exists at the RBC junctional complex that involves interactions between spectrin, adducin, and band 3. PMID:20056793

Analysis of novel sph (spherocytosis) alleles in mice reveals allele-specific loss of band 3 and adducin in alpha-spectrin-deficient red cells.

PubMed

Robledo, Raymond F; Lambert, Amy J; Birkenmeier, Connie S; Cirlan, Marius V; Cirlan, Andreea Flavia M; Campagna, Dean R; Lux, Samuel E; Peters, Luanne L

2010-03-04

Five spontaneous, allelic mutations in the alpha-spectrin gene, Spna1, have been identified in mice (spherocytosis [sph], sph(1J), sph(2J), sph(2BC), sph(Dem)). All cause severe hemolytic anemia. Here, analysis of 3 new alleles reveals previously unknown consequences of red blood cell (RBC) spectrin deficiency. In sph(3J), a missense mutation (H2012Y) in repeat 19 introduces a cryptic splice site resulting in premature termination of translation. In sph(Ihj), a premature stop codon occurs (Q1853Stop) in repeat 18. Both mutations result in markedly reduced RBC membrane spectrin content, decreased band 3, and absent beta-adducin. Reevaluation of available, previously described sph alleles reveals band 3 and adducin deficiency as well. In sph(4J), a missense mutation occurs in the C-terminal EF hand domain (C2384Y). Notably, an equally severe hemolytic anemia occurs despite minimally decreased membrane spectrin with normal band 3 levels and present, although reduced, beta-adducin. The severity of anemia in sph(4J) indicates that the highly conserved cysteine residue at the C-terminus of alpha-spectrin participates in interactions critical to membrane stability. The data reinforce the notion that a membrane bridge in addition to the classic protein 4.1-p55-glycophorin C linkage exists at the RBC junctional complex that involves interactions between spectrin, adducin, and band 3.

Atomic detail brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions.

PubMed

Mereghetti, Paolo; Wade, Rebecca C

2012-07-26

High macromolecular concentrations are a distinguishing feature of living organisms. Understanding how the high concentration of solutes affects the dynamic properties of biological macromolecules is fundamental for the comprehension of biological processes in living systems. In this paper, we describe the implementation of mean field models of translational and rotational hydrodynamic interactions into an atomically detailed many-protein brownian dynamics simulation method. Concentrated solutions (30-40% volume fraction) of myoglobin, hemoglobin A, and sickle cell hemoglobin S were simulated, and static structure factors, oligomer formation, and translational and rotational self-diffusion coefficients were computed. Good agreement of computed properties with available experimental data was obtained. The results show the importance of both solvent mediated interactions and weak protein-protein interactions for accurately describing the dynamics and the association properties of concentrated protein solutions. Specifically, they show a qualitative difference in the translational and rotational dynamics of the systems studied. Although the translational diffusion coefficient is controlled by macromolecular shape and hydrodynamic interactions, the rotational diffusion coefficient is affected by macromolecular shape, direct intermolecular interactions, and both translational and rotational hydrodynamic interactions.

Source characterization of underground explosions from hydrodynamic-to-elastic coupling simulations

NASA Astrophysics Data System (ADS)

Chiang, A.; Pitarka, A.; Ford, S. R.; Ezzedine, S. M.; Vorobiev, O.

2017-12-01

A major improvement in ground motion simulation capabilities for underground explosion monitoring during the first phase of the Source Physics Experiment (SPE) is the development of a wave propagation solver that can propagate explosion generated non-linear near field ground motions to the far-field. The calculation is done using a hybrid modeling approach with a one-way hydrodynamic-to-elastic coupling in three dimensions where near-field motions are computed using GEODYN-L, a Lagrangian hydrodynamics code, and then passed to WPP, an elastic finite-difference code for seismic waveform modeling. The advancement in ground motion simulation capabilities gives us the opportunity to assess moment tensor inversion of a realistic volumetric source with near-field effects in a controlled setting, where we can evaluate the recovered source properties as a function of modeling parameters (i.e. velocity model) and can provide insights into previous source studies on SPE Phase I chemical shots and other historical nuclear explosions. For example the moment tensor inversion of far-field SPE seismic data demonstrated while vertical motions are well-modeled using existing velocity models large misfits still persist in predicting tangential shear wave motions from explosions. One possible explanation we can explore is errors and uncertainties from the underlying Earth model. Here we investigate the recovered moment tensor solution, particularly on the non-volumetric component, by inverting far-field ground motions simulated from physics-based explosion source models in fractured material, where the physics-based source models are based on the modeling of SPE-4P, SPE-5 and SPE-6 near-field data. The hybrid modeling approach provides new prospects in modeling explosion source and understanding the uncertainties associated with it.

A conservative MHD scheme on unstructured Lagrangian grids for Z-pinch hydrodynamic simulations

NASA Astrophysics Data System (ADS)

Wu, Fuyuan; Ramis, Rafael; Li, Zhenghong

2018-03-01

A new algorithm to model resistive magnetohydrodynamics (MHD) in Z-pinches has been developed. Two-dimensional axisymmetric geometry with azimuthal magnetic field Bθ is considered. Discretization is carried out using unstructured meshes made up of arbitrarily connected polygons. The algorithm is fully conservative for mass, momentum, and energy. Matter energy and magnetic energy are managed separately. The diffusion of magnetic field is solved using a derivative of the Symmetric-Semi-Implicit scheme, Livne et al. (1985) [23], where unconditional stability is obtained without needing to solve large sparse systems of equations. This MHD package has been integrated into the radiation-hydrodynamics code MULTI-2D, Ramis et al. (2009) [20], that includes hydrodynamics, laser energy deposition, heat conduction, and radiation transport. This setup allows to simulate Z-pinch configurations relevant for Inertial Confinement Fusion.

Hydrodynamic suppression of phase separation in active suspensions.

PubMed

Matas-Navarro, Ricard; Golestanian, Ramin; Liverpool, Tanniemola B; Fielding, Suzanne M

2014-09-01

We simulate with hydrodynamics a suspension of active disks squirming through a Newtonian fluid. We explore numerically the full range of squirmer area fractions from dilute to close packed and show that "motility induced phase separation," which was recently proposed to arise generically in active matter, and which has been seen in simulations of active Brownian disks, is strongly suppressed by hydrodynamic interactions. We give an argument for why this should be the case and support it with counterpart simulations of active Brownian disks in a parameter regime that provides a closer counterpart to hydrodynamic suspensions than in previous studies.

Relativistic anisotropic hydrodynamics

NASA Astrophysics Data System (ADS)

Alqahtani, Mubarak; Nopoush, Mohammad; Strickland, Michael

2018-07-01

In this paper we review recent progress in relativistic anisotropic hydrodynamics. We begin with a pedagogical introduction to the topic which takes into account the advances in our understanding of this topic since its inception. We consider both conformal and non-conformal systems and demonstrate how one can implement a realistic equation of state using a quasiparticle approach. We then consider the inclusion of non-spheroidal (non-ellipsoidal) corrections to leading-order anisotropic hydrodynamics and present the findings of the resulting second-order viscous anisotropic hydrodynamics framework. We compare the results obtained in both the conformal and non-conformal cases with exact solutions to the Boltzmann equation and demonstrate that, in all known cases, anisotropic hydrodynamics best reproduces the exact solutions. Based on this success, we then discuss the phenomenological application of anisotropic hydrodynamics. Along these lines, we review techniques which can be used to convert a momentum-space anisotropic fluid into hadronic degrees of freedom by generalizing the original idea of Cooper-Frye freeze-out to momentum-space anisotropic systems. And, finally, we present phenomenological results of 3 + 1 d quasiparticle anisotropic hydrodynamic simulations and compare them to experimental data produced in 2.76 TeV Pb-Pb collisions at the LHC. Our results indicate that anisotropic hydrodynamics provides a promising framework for describing the dynamics of the momentum-space anisotropic QGP created in heavy-ion collisions.

Does Explosive Nuclear Burning Occur in Tidal Disruption Events of White Dwarfs by Intermediate-mass Black Holes?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tanikawa, Ataru; Sato, Yushi; Hachisu, Izumi

We investigate nucleosynthesis in tidal disruption events (TDEs) of white dwarfs (WDs) by intermediate-mass black holes. We consider various types of WDs with different masses and compositions by means of three-dimensional (3D) smoothed particle hydrodynamics (SPH) simulations. We model these WDs with different numbers of SPH particles, N , from a few 10{sup 4} to a few 10{sup 7} in order to check mass resolution convergence, where SPH simulations with N > 10{sup 7} (or a space resolution of several 10{sup 6} cm) have unprecedentedly high resolution in this kind of simulation. We find that nuclear reactions become less activemore » with increasing N and that these nuclear reactions are excited by spurious heating due to low resolution. Moreover, we find no shock wave generation. In order to investigate the reason for the absence of a shock wave, we additionally perform one-dimensional (1D) SPH and mesh-based simulations with a space resolution ranging from 10{sup 4} to 10{sup 7} cm, using a characteristic flow structure extracted from the 3D SPH simulations. We find shock waves in these 1D high-resolution simulations, one of which triggers a detonation wave. However, we must be careful of the fact that, if the shock wave emerged in an outer region, it could not trigger the detonation wave due to low density. Note that the 1D initial conditions lack accuracy to precisely determine where a shock wave emerges. We need to perform 3D simulations with ≲10{sup 6} cm space resolution in order to conclude that WD TDEs become optical transients powered by radioactive nuclei.« less

Topology of Large-Scale Structure by Galaxy Type: Hydrodynamic Simulations

NASA Astrophysics Data System (ADS)

Gott, J. Richard, III; Cen, Renyue; Ostriker, Jeremiah P.

1996-07-01

The topology of large-scale structure is studied as a function of galaxy type using the genus statistic. In hydrodynamical cosmological cold dark matter simulations, galaxies form on caustic surfaces (Zeldovich pancakes) and then slowly drain onto filaments and clusters. The earliest forming galaxies in the simulations (defined as "ellipticals") are thus seen at the present epoch preferentially in clusters (tending toward a meatball topology), while the latest forming galaxies (defined as "spirals") are seen currently in a spongelike topology. The topology is measured by the genus (number of "doughnut" holes minus number of isolated regions) of the smoothed density-contour surfaces. The measured genus curve for all galaxies as a function of density obeys approximately the theoretical curve expected for random- phase initial conditions, but the early-forming elliptical galaxies show a shift toward a meatball topology relative to the late-forming spirals. Simulations using standard biasing schemes fail to show such an effect. Large observational samples separated by galaxy type could be used to test for this effect.

NIF laboratory astrophysics simulations investigating the effects of a radiative shock on hydrodynamic instabilities

NASA Astrophysics Data System (ADS)

Angulo, A. A.; Kuranz, C. C.; Drake, R. P.; Huntington, C. M.; Park, H.-S.; Remington, B. A.; Kalantar, D.; MacLaren, S.; Raman, K.; Miles, A.; Trantham, Matthew; Kline, J. L.; Flippo, K.; Doss, F. W.; Shvarts, D.

2016-10-01

This poster will describe simulations based on results from ongoing laboratory astrophysics experiments at the National Ignition Facility (NIF) relevant to the effects of radiative shock on hydrodynamically unstable surfaces. The experiments performed on NIF uniquely provide the necessary conditions required to emulate radiative shock that occurs in astrophysical systems. The core-collapse explosions of red supergiant stars is such an example wherein the interaction between the supernova ejecta and the circumstellar medium creates a region susceptible to Rayleigh-Taylor (R-T) instabilities. Radiative and nonradiative experiments were performed to show that R-T growth should be reduced by the effects of the radiative shocks that occur during this core-collapse. Simulations were performed using the radiation hydrodynamics code Hyades using the experimental conditions to find the mean interface acceleration of the instability and then further analyzed in the buoyancy drag model to observe how the material expansion contributes to the mix-layer growth. This work is funded by the NNSA-DS and SC-OFES Joint Program in High-Energy-Density Laboratory Plasmas under Grant Number DE-FG52-09NA29548.

Visualizing SPH Cataclysmic Variable Accretion Disk Simulations with Blender

NASA Astrophysics Data System (ADS)

Kent, Brian R.; Wood, Matthew A.

2015-01-01

We present innovative ways to use Blender, a 3D graphics package, to visualize smoothed particle hydrodynamics particle data of cataclysmic variable accretion disks. We focus on the methods of shape key data constructs to increasedata i/o and manipulation speed. The implementation of the methods outlined allow for compositing of the various visualization layers into a final animation. The viewing of the disk in 3D from different angles can allow for a visual analysisof the physical system and orbits. The techniques have a wide ranging set of applications in astronomical visualization,including both observation and theoretical data.

Modeling and Simulation of Ceramic Arrays to Improve Ballaistic Performance

DTIC Science & Technology

2013-10-01

are modeled using SPH elements. Model validation runs with monolithic SiC tiles are conducted based on the DoP experiments described in reference...TERMS ,30cal AP M2 Projectile, 762x39 PS Projectile, SPH , Aluminum 5083, SiC, DoP Expeminets, AutoDyn Simulations, Tile Gap 16. SECURITY...range 700 m/s to 1000 m/s are modeled using SPH elements. □ Model validation runs with monolithic SiC tiles are conducted based on the DoP

Progress and Challenges in SPH Simulations of Disk Galaxy Formation: The Combined Role of Resolution and the Star Formation Density Threshold

NASA Astrophysics Data System (ADS)

Mayer, L.

2012-07-01

We review progress in cosmological SPH simulations of disk galaxy formation. We discuss the role of numerical resolution and sub-grid recipes of star formation and feedback from supernovae, higlighting the important role of a high star formation density threshold comparable to that of star forming molecular gas phase. Two recent succesfull examples, in simulations of the formation of gas-rich bulgeless dwarf galaxies and in simulations of late-type spirals (the ERIS simulations), are presented and discussed. In the ERIS simulations, already in the progenitors at z = 3 the resolution is above the threshold indicated by previous idealized numerical experiments as necessary to minimize numerical angular momentum loss (Kaufmann et al. 2007). A high star formation density threshold maintains an inhomogeneous interstellar medium, where star formation is clustered, and thus the local effect of supernovae feedback is enhanced. As a result, outflows are naturally generated removing 2/3 of the baryons in galaxies with Vvir˜50 km/s and ˜ 30% of the baryons in galaxies with (Vvir ˜ 150 km/s). Low angular momentum baryons are preferentially removed since the strongest bursts of star formation occur predominantly near the center, especially after a merger event. This produces pure exponential disks or small bulges depending on galaxy mass, and, correspondingly, slowly rising or nearly flat rotation curves that match those of observed disk galaxies. In dwarfs the rapid mass removal by outflows generates a core-like distribution in the dark matter. Furthermore, contrary to the common picture, in the ERIS spiral galaxies a bar/pseudobulge forms rapidly, and not secularly, as a result of mergers and interactions at high-z.

Cloning and characterization of a shrimp clip domain serine protease homolog (c-SPH) as a cell adhesion molecule.

PubMed

Lin, Chun-Yu; Hu, Kuang-Yu; Ho, Shih-Hu; Song, Yen-Ling

2006-01-01

Clip domain serine protease homologs (c-SPHs) are involved in various innate immune functions in arthropods such as antimicrobial activity, cell adhesion, pattern recognition, opsonization, and regulation of the prophenoloxidase system. In the present study, we cloned a c-SPH cDNA from tiger shrimp (Penaeus monodon) hemocytes. It is 1337 bp in length with a coding region of 1068 bp consisting a protein of 355 amino acid residues. The deduced protein includes one clip domain and one catalytically inactive serine protease-like (SP-like) domain. Its molecular weight is estimated to be 38 kDa with an isoelectric point of 7.9. The predicted cutting site of the signal peptide is located between Gly(21) and Gln(22). We aligned 15 single clip domain SPH protein sequences from 12 arthropod species; the identity of these clip domains is low and that of SP-like domains is from 34% to 46%. The conserved regions are located near the amino acid residues which served as substrate interaction sites in catalytically active serine protease. Phylogenetically, the tiger shrimp c-SPH is most similar to a low molecular mass masquerade-like protein of crayfish, but less similar to c-SPHs in Chelicerata and Insecta. Nested reverse transcription polymerase chain reaction (RT-PCR) revealed that c-SPH mRNA is expressed most in tissues with the highest hemocyte abundance. Antimicrobial and opsonization activities of the molecule were not detected. The expression of c-SPH mRNA in hemocytes was up-regulated at the 12-day post beta-glucan immersion. Recombinant c-SPH could significantly enhance hemocyte adhesion. The result suggests that the shrimp c-SPH protein plays a role in innate immunity.

Stochastic simulation of reaction-diffusion systems: A fluctuating-hydrodynamics approach

NASA Astrophysics Data System (ADS)

Kim, Changho; Nonaka, Andy; Bell, John B.; Garcia, Alejandro L.; Donev, Aleksandar

2017-03-01

We develop numerical methods for stochastic reaction-diffusion systems based on approaches used for fluctuating hydrodynamics (FHD). For hydrodynamic systems, the FHD formulation is formally described by stochastic partial differential equations (SPDEs). In the reaction-diffusion systems we consider, our model becomes similar to the reaction-diffusion master equation (RDME) description when our SPDEs are spatially discretized and reactions are modeled as a source term having Poisson fluctuations. However, unlike the RDME, which becomes prohibitively expensive for an increasing number of molecules, our FHD-based description naturally extends from the regime where fluctuations are strong, i.e., each mesoscopic cell has few (reactive) molecules, to regimes with moderate or weak fluctuations, and ultimately to the deterministic limit. By treating diffusion implicitly, we avoid the severe restriction on time step size that limits all methods based on explicit treatments of diffusion and construct numerical methods that are more efficient than RDME methods, without compromising accuracy. Guided by an analysis of the accuracy of the distribution of steady-state fluctuations for the linearized reaction-diffusion model, we construct several two-stage (predictor-corrector) schemes, where diffusion is treated using a stochastic Crank-Nicolson method, and reactions are handled by the stochastic simulation algorithm of Gillespie or a weakly second-order tau leaping method. We find that an implicit midpoint tau leaping scheme attains second-order weak accuracy in the linearized setting and gives an accurate and stable structure factor for a time step size of an order of magnitude larger than the hopping time scale of diffusing molecules. We study the numerical accuracy of our methods for the Schlögl reaction-diffusion model both in and out of thermodynamic equilibrium. We demonstrate and quantify the importance of thermodynamic fluctuations to the formation of a two

Revealing the Physics of Galactic Winds Through Massively-Parallel Hydrodynamics Simulations

NASA Astrophysics Data System (ADS)

Schneider, Evan Elizabeth

This thesis documents the hydrodynamics code Cholla and a numerical study of multiphase galactic winds. Cholla is a massively-parallel, GPU-based code designed for astrophysical simulations that is freely available to the astrophysics community. A static-mesh Eulerian code, Cholla is ideally suited to carrying out massive simulations (> 20483 cells) that require very high resolution. The code incorporates state-of-the-art hydrodynamics algorithms including third-order spatial reconstruction, exact and linearized Riemann solvers, and unsplit integration algorithms that account for transverse fluxes on multidimensional grids. Operator-split radiative cooling and a dual-energy formalism for high mach number flows are also included. An extensive test suite demonstrates Cholla's superior ability to model shocks and discontinuities, while the GPU-native design makes the code extremely computationally efficient - speeds of 5-10 million cell updates per GPU-second are typical on current hardware for 3D simulations with all of the aforementioned physics. The latter half of this work comprises a comprehensive study of the mixing between a hot, supernova-driven wind and cooler clouds representative of those observed in multiphase galactic winds. Both adiabatic and radiatively-cooling clouds are investigated. The analytic theory of cloud-crushing is applied to the problem, and adiabatic turbulent clouds are found to be mixed with the hot wind on similar timescales as the classic spherical case (4-5 t cc) with an appropriate rescaling of the cloud-crushing time. Radiatively cooling clouds survive considerably longer, and the differences in evolution between turbulent and spherical clouds cannot be reconciled with a simple rescaling. The rapid incorporation of low-density material into the hot wind implies efficient mass-loading of hot phases of galactic winds. At the same time, the extreme compression of high-density cloud material leads to long-lived but slow-moving clumps

Hybrid Eulerian and Lagrangian Simulation of Steep and Breaking Waves and Surface Fluxes in High Winds

DTIC Science & Technology

2011-09-30

simulation provides boundary condition to the SPH simulation in a sub- domain. For the test with surface wave propagation, the free surface and the...This project aims at developing an advanced simulation tool for multi-fluids free - surface flows that can be used to study the fundamental physics...of horizontal velocity(normalized by wave phase speed c) obtained from SPH simulation and the corresponding free surface obtained from LSM

Application of PCDA/SPH/CHO/Lysine vesicles to detect pathogenic bacteria in chicken.

PubMed

de Oliveira, Taíla V; Soares, Nilda de F F; de Andrade, Nélio J; Silva, Deusanilde J; Medeiros, Eber Antônio A; Badaró, Amanda T

2015-04-01

During the course of infection, Salmonella must successively survive the harsh acid stress of the stomach and multiply into a mild acidic compartment within macrophages. Inducible amino acid decarboxylases are known to promote adaptation to acidic environments, as lysine decarboxylation to cadaverine. The idea of Salmonella defenses responses could be employed in systems as polydiacetylene (PDA) to detect this pathogen so important to public health system. Beside that PDA is an important substance because of the unique optical property; that undergoes a colorimetric transitions by various external stimuli. Therefore 10,12-pentacosadyinoic acid (PCDA)/Sphingomyelin(SPH)/Cholesterol(CHO)/Lysine system was tested to determine the colorimetric response induced by Salmonella choleraesuis. PCDA/SPH/CHO/Lysine vesicles showed a colour change even in low S. choleraesuis concentration present in laboratory conditions and in chicken meat. Thus, this work showed a PCDA/SPH/CHO/Lysine vesicle application to simplify routine analyses in food industry, as chicken meat industry. Copyright © 2014 Elsevier Ltd. All rights reserved.

Resolution convergence in cosmological hydrodynamical simulations using adaptive mesh refinement

NASA Astrophysics Data System (ADS)

Snaith, Owain N.; Park, Changbom; Kim, Juhan; Rosdahl, Joakim

2018-06-01

We have explored the evolution of gas distributions from cosmological simulations carried out using the RAMSES adaptive mesh refinement (AMR) code, to explore the effects of resolution on cosmological hydrodynamical simulations. It is vital to understand the effect of both the resolution of initial conditions (ICs) and the final resolution of the simulation. Lower initial resolution simulations tend to produce smaller numbers of low-mass structures. This will strongly affect the assembly history of objects, and has the same effect of simulating different cosmologies. The resolution of ICs is an important factor in simulations, even with a fixed maximum spatial resolution. The power spectrum of gas in simulations using AMR diverges strongly from the fixed grid approach - with more power on small scales in the AMR simulations - even at fixed physical resolution and also produces offsets in the star formation at specific epochs. This is because before certain times the upper grid levels are held back to maintain approximately fixed physical resolution, and to mimic the natural evolution of dark matter only simulations. Although the impact of hold-back falls with increasing spatial and IC resolutions, the offsets in the star formation remain down to a spatial resolution of 1 kpc. These offsets are of the order of 10-20 per cent, which is below the uncertainty in the implemented physics but are expected to affect the detailed properties of galaxies. We have implemented a new grid-hold-back approach to minimize the impact of hold-back on the star formation rate.

Application of a coupled smoothed particle hydrodynamics (SPH) and coarse-grained (CG) numerical modelling approach to study three-dimensional (3-D) deformations of single cells of different food-plant materials during drying.

PubMed

Rathnayaka, C M; Karunasena, H C P; Senadeera, W; Gu, Y T

2018-03-14

Numerical modelling has gained popularity in many science and engineering streams due to the economic feasibility and advanced analytical features compared to conventional experimental and theoretical models. Food drying is one of the areas where numerical modelling is increasingly applied to improve drying process performance and product quality. This investigation applies a three dimensional (3-D) Smoothed Particle Hydrodynamics (SPH) and Coarse-Grained (CG) numerical approach to predict the morphological changes of different categories of food-plant cells such as apple, grape, potato and carrot during drying. To validate the model predictions, experimental findings from in-house experimental procedures (for apple) and sources of literature (for grape, potato and carrot) have been utilised. The subsequent comaprison indicate that the model predictions demonstrate a reasonable agreement with the experimental findings, both qualitatively and quantitatively. In this numerical model, a higher computational accuracy has been maintained by limiting the consistency error below 1% for all four cell types. The proposed meshfree-based approach is well-equipped to predict the morphological changes of plant cellular structure over a wide range of moisture contents (10% to 100% dry basis). Compared to the previous 2-D meshfree-based models developed for plant cell drying, the proposed model can draw more useful insights on the morphological behaviour due to the 3-D nature of the model. In addition, the proposed computational modelling approach has a high potential to be used as a comprehensive tool in many other tissue morphology related investigations.

SIDM on FIRE: hydrodynamical self-interacting dark matter simulations of low-mass dwarf galaxies

NASA Astrophysics Data System (ADS)

Robles, Victor H.; Bullock, James S.; Elbert, Oliver D.; Fitts, Alex; González-Samaniego, Alejandro; Boylan-Kolchin, Michael; Hopkins, Philip F.; Faucher-Giguère, Claude-André; Kereš, Dušan; Hayward, Christopher C.

2017-12-01

We compare a suite of four simulated dwarf galaxies formed in 1010 M⊙ haloes of collisionless cold dark matter (CDM) with galaxies simulated in the same haloes with an identical galaxy formation model but a non-zero cross-section for DM self-interactions. These cosmological zoom-in simulations are part of the Feedback In Realistic Environments (FIRE) project and utilize the FIRE-2 model for hydrodynamics and galaxy formation physics. We find the stellar masses of the galaxies formed in self-interacting dark matter (SIDM) with σ/m = 1 cm2 g-1 are very similar to those in CDM (spanning M⋆ ≈ 105.7-7.0M⊙) and all runs lie on a similar stellar mass-size relation. The logarithmic DM density slope (α = d log ρ/d log r) in the central 250-500 pc remains steeper than α = -0.8 for the CDM-Hydro simulations with stellar mass M⋆ ∼ 106.6 M⊙ and core-like in the most massive galaxy. In contrast, every SIDM hydrodynamic simulation yields a flatter profile, with α > -0.4. Moreover, the central density profiles predicted in SIDM runs without baryons are similar to the SIDM runs that include FIRE-2 baryonic physics. Thus, SIDM appears to be much more robust to the inclusion of (potentially uncertain) baryonic physics than CDM on this mass scale, suggesting that SIDM will be easier to falsify than CDM using low-mass galaxies. Our FIRE simulations predict that galaxies less massive than M⋆ ≲ 3 × 106 M⊙ provide potentially ideal targets for discriminating models, with SIDM producing substantial cores in such tiny galaxies and CDM producing cusps.

Direct numerical simulation of transitional hydrodynamics of the cerebrospinal fluid in Chiari I malformation: The role of cranio-vertebral junction.

PubMed

Jain, Kartik; Ringstad, Geir; Eide, Per-Kristian; Mardal, Kent-André

2017-09-01

Obstruction to the cerebrospinal fluid (CSF) outflow caused by the herniation of cerebellar tonsils as a result of Chiari malformation type I leads to altered CSF hydrodynamics. This contribution explores the minutest characteristics of the CSF hydrodynamics in cervical subarachnoid space (SAS) of a healthy subject and 2 Chiari patients by performing highly resolved direct numerical simulation. The lattice Boltzmann method is used for the simulations because of its scalability on modern supercomputers that allow us to simulate up to approximately 10 9 cells while resolving the Kolmogorov microscales. The results depict that whereas the complex CSF flow remains largely laminar in the SAS of a healthy subject, constriction of the cranio-vertebral junction in Chiari I patients causes manifold fluctuations in the hydrodynamics of the CSF. These fluctuations resemble a flow that is in a transitional regime rather than laminar or fully developed turbulence. The fluctuations confine near the cranio-vertebral junction and are triggered due to the tonsillar herniation, which perturbs the flow as a result of altered anatomy of the SAS. Copyright © 2016 John Wiley & Sons, Ltd.

Synthesis of Aromatic Thiolate-Protected Gold Nanomolecules by Core Conversion: The Case of Au36(SPh-tBu)24.

PubMed

Theivendran, Shevanuja; Dass, Amala

2017-08-01

Ultrasmall nanomolecules (<2 nm) such as Au 25 (SCH 2 CH 2 Ph) 18 , Au 38 (SCH 2 CH 2 Ph) 24 , and Au 144 (SCH 2 CH 2 Ph) 60 are well studied and can be prepared using established synthetic procedures. No such synthetic protocols that result in high yield products from commercially available starting materials exist for Au 36 (SPh-X) 24 . Here, we report a synthetic procedure for the large-scale synthesis of highly stable Au 36 (SPh-X) 24 with a yield of ∼42%. Au 36 (SPh-X) 24 was conveniently synthesized by using tert-butylbenzenethiol (HSPh-tBu, TBBT) as the ligand, giving a more stable product with better shelf life and higher yield than previously reported for making Au 36 (SPh) 24 from thiophenol (PhSH). The choice of thiol, solvent, and reaction conditions were modified for the optimization of the synthetic procedure. The purposes of this work are to (1) optimize the existing procedure to obtain stable product with better yield, (2) develop a scalable synthetic procedure, (3) demonstrate the superior stability of Au 36 (SPh-tBu) 24 when compared to Au 36 (SPh) 24 , and (4) demonstrate the reproducibility and robustness of the optimized synthetic procedure.

Multi-Dimensional Full Boltzmann-Neutrino-Radiation Hydrodynamic Simulations and Their Detailed Comparisons with Monte-Carlo Methods in Core Collapse Supernovae

NASA Astrophysics Data System (ADS)

Nagakura, H.; Richers, S.; Ott, C. D.; Iwakami, W.; Furusawa, S.; Sumiyoshi, K.; Yamada, S.; Matsufuru, H.; Imakura, A.

2016-10-01

We have developed a 7-dimensional Full Boltzmann-neutrino-radiation-hydrodynamical code and carried out ab-initio axisymmetric CCSNe simulations. I will talk about main results of our simulations and also discuss current ongoing projects.

Numerical calculation of protein-ligand binding rates through solution of the Smoluchowski equation using smoothed particle hydrodynamics

DOE PAGES

Pan, Wenxiao; Daily, Michael; Baker, Nathan A.

2015-05-07

Background: The calculation of diffusion-controlled ligand binding rates is important for understanding enzyme mechanisms as well as designing enzyme inhibitors. Methods: We demonstrate the accuracy and effectiveness of a Lagrangian particle-based method, smoothed particle hydrodynamics (SPH), to study diffusion in biomolecular systems by numerically solving the time-dependent Smoluchowski equation for continuum diffusion. Unlike previous studies, a reactive Robin boundary condition (BC), rather than the absolute absorbing (Dirichlet) BC, is considered on the reactive boundaries. This new BC treatment allows for the analysis of enzymes with “imperfect” reaction rates. Results: The numerical method is first verified in simple systems and thenmore » applied to the calculation of ligand binding to a mouse acetylcholinesterase (mAChE) monomer. Rates for inhibitor binding to mAChE are calculated at various ionic strengths and compared with experiment and other numerical methods. We find that imposition of the Robin BC improves agreement between calculated and experimental reaction rates. Conclusions: Although this initial application focuses on a single monomer system, our new method provides a framework to explore broader applications of SPH in larger-scale biomolecular complexes by taking advantage of its Lagrangian particle-based nature.« less

Au36(SPh)24 nanomolecules: X-ray crystal structure, optical spectroscopy, electrochemistry, and theoretical analysis.

PubMed

Nimmala, Praneeth Reddy; Knoppe, Stefan; Jupally, Vijay Reddy; Delcamp, Jared H; Aikens, Christine M; Dass, Amala

2014-12-11

The physicochemical properties of gold:thiolate nanomolecules depend on their crystal structure and the capping ligands. The effects of protecting ligands on the crystal structure of the nanomolecules are of high interest in this area of research. Here we report the crystal structure of an all aromatic thiophenolate-capped Au36(SPh)24 nanomolecule, which has a face-centered cubic (fcc) core similar to other nanomolecules such as Au36(SPh-tBu)24 and Au36(SC5H9)24 with the same number of gold atoms and ligands. The results support the idea that a stable core remains intact even when the capping ligand is varied. We also correct our earlier assignment of "Au36(SPh)23" which was determined based on MALDI mass spectrometry which is more prone to fragmentation than ESI mass spectrometry. We show that ESI mass spectrometry gives the correct assignment of Au36(SPh)24, supporting the X-ray crystal structure. The electronic structure of the title compound was computed at different levels of theory (PBE, LDA, and LB94) using the coordinates extracted from the single crystal X-ray diffraction data. The optical and electrochemical properties were determined from experimental data using UV-vis spectroscopy, cyclic voltammetry, and differential pulse voltammetry. Au36(SPh)24 shows a broad electrochemical gap near 2 V, a desirable optical gap of ∼1.75 eV for dye-sensitized solar cell applications, as well as appropriately positioned electrochemical potentials for many electrocatalytic reactions.

A smoothed particle hydrodynamics model for droplet and film flow on smooth and rough fracture surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kordilla, Jannes; Tartakovsky, Alexandre M.; Geyer, Tobias

2013-09-01

Flow on fracture surfaces has been identified by many authors as an important flow process in unsaturated fractured rock formations. Given the complexity of flow dynamics on such small scales, robust numerical methods have to be employed in order to capture the highly dynamic interfaces and flow intermittency. In this work we present microscale free-surface flow simulations using a three-dimensional multiphase Smoothed Particle Hydrodynamics (SPH) code. Pairwise solid-fluid and fluid-fluid interaction forces are used to control the wetting behavior and cover a wide range of static and transient contact angles as well as Reynolds numbers encountered in droplet flow onmore » rock surfaces. We validate our model via comparison with existing empirical and semi-analyical solutions for droplet flow. We use the model to investigate the occurence of adsorbed trailing films of droplets under various flow conditions and its importance for the flow dynamics when films and droplets coexist. We show that flow velocities are higher on prewetted surfaces covered by a thin film which is qualitatively attributed to the enhanced dynamic wetting and dewetting at the trailing and advancing contact line.« less

Dynamics and Chemistry in Jovian Atmospheres: 2D Hydrodynamical Simulations

NASA Astrophysics Data System (ADS)

Bordwell, B. R.; Brown, B. P.; Oishi, J.

2016-12-01

A key component of our understanding of the formation and evolution of planetary systems is chemical composition. Problematically, however, in the atmospheres of cooler gas giants, dynamics on the same timescale as chemical reactions pull molecular abundances out of thermochemical equilibrium. These disequilibrium abundances are treated using what is known as the "quench" approximation, based upon the mixing length theory of convection. The validity of this approximation is questionable, though, as the atmospheres of gas giants encompass two distinct dynamic regimes: convective and radiative. To resolve this issue, we conduct 2D hydrodynamical simulations using the state-of-the-art pseudospectral simulation framework Dedalus. In these simulations, we solve the fully compressible equations of fluid motion in a local slab geometry that mimics the structure of a planetary atmosphere (convective zone underlying a radiative zone). Through the inclusion of passive tracers, we explore the transport properties of both regimes, and assess the validity of the classical eddy diffusion parameterization. With the addition of active tracers, we examine the interactions between dynamical and chemical processes, and generate prescriptions for the observational community. By providing insight into mixing and feedback mechanisms in Jovian atmospheres, this research lays a solid foundation for future global simulations and the construction of physically-sound models for current and future observations.

Hydrodynamical simulations of strong tides in astrophysical systems

NASA Astrophysics Data System (ADS)

Guillochon, James

2013-07-01

At the simplest level, gravitational sources are considered to be point-like and in solitude, with a radial force that falls off as r -2. In reality, all astrophysical objects aside from black holes are extended in space, and can be deformed by the tidal forces arising from the proximity of companion objects with large average densities. When these forces are weak, the response of an object to a tide can be through a decomposition into basis functions, but this approach fails when the tide is strong enough to deform an object by a distance equal to its own size. Under these circumstances, a hydrodynamical representation of the object is required to understand the true tidal response. In this thesis, we present a number of examples of physical systems in which tides dominate the dynamics. First, we consider the case of a star that encounters a supermassive black hole (SMBH) in a deeply penetrating encounter, resulting in a dramatic compression that produces shocks that would be observable in the X-ray. Second, we present the results of hydrodynamical simulations that demonstrate a new mechanism for igniting Type Ia supernovae from binary systems composed of two white dwarfs undergoing Roche-lobe overflow. Third, we investigate the survival prospects of giant planets that have been scattered into highly eccentricity orbits and are exposed to a strong tide applied by their parent star. Fourth, we systematically map the fallback rate resulting from the tidal disruptions of stars by SMBHs. Finally, we use what we have learned about the feeding rate to model determine the highest-likelihood model for an observed prototypical tidal disruption event.

Shadowfax: Moving mesh hydrodynamical integration code

NASA Astrophysics Data System (ADS)

Vandenbroucke, Bert

2016-05-01

Shadowfax simulates galaxy evolution. Written in object-oriented modular C++, it evolves a mixture of gas, subject to the laws of hydrodynamics and gravity, and any collisionless fluid only subject to gravity, such as cold dark matter or stars. For the hydrodynamical integration, it makes use of a (co-) moving Lagrangian mesh. The code has a 2D and 3D version, contains utility programs to generate initial conditions and visualize simulation snapshots, and its input/output is compatible with a number of other simulation codes, e.g. Gadget2 (ascl:0003.001) and GIZMO (ascl:1410.003).

RAPID OPTIMAL SPH PARTICLE DISTRIBUTIONS IN SPHERICAL GEOMETRIES FOR CREATING ASTROPHYSICAL INITIAL CONDITIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Raskin, Cody; Owen, J. Michael

2016-04-01

Creating spherical initial conditions in smoothed particle hydrodynamics simulations that are spherically conformal is a difficult task. Here, we describe two algorithmic methods for evenly distributing points on surfaces that when paired can be used to build three-dimensional spherical objects with optimal equipartition of volume between particles, commensurate with an arbitrary radial density function. We demonstrate the efficacy of our method against stretched lattice arrangements on the metrics of hydrodynamic stability, spherical conformity, and the harmonic power distribution of gravitational settling oscillations. We further demonstrate how our method is highly optimized for simulating multi-material spheres, such as planets with core–mantlemore » boundaries.« less

RICH: OPEN-SOURCE HYDRODYNAMIC SIMULATION ON A MOVING VORONOI MESH

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yalinewich, Almog; Steinberg, Elad; Sari, Re’em

2015-02-01

We present here RICH, a state-of-the-art two-dimensional hydrodynamic code based on Godunov’s method, on an unstructured moving mesh (the acronym stands for Racah Institute Computational Hydrodynamics). This code is largely based on the code AREPO. It differs from AREPO in the interpolation and time-advancement schemeS as well as a novel parallelization scheme based on Voronoi tessellation. Using our code, we study the pros and cons of a moving mesh (in comparison to a static mesh). We also compare its accuracy to other codes. Specifically, we show that our implementation of external sources and time-advancement scheme is more accurate and robustmore » than is AREPO when the mesh is allowed to move. We performed a parameter study of the cell rounding mechanism (Lloyd iterations) and its effects. We find that in most cases a moving mesh gives better results than a static mesh, but it is not universally true. In the case where matter moves in one way and a sound wave is traveling in the other way (such that relative to the grid the wave is not moving) a static mesh gives better results than a moving mesh. We perform an analytic analysis for finite difference schemes that reveals that a Lagrangian simulation is better than a Eulerian simulation in the case of a highly supersonic flow. Moreover, we show that Voronoi-based moving mesh schemes suffer from an error, which is resolution independent, due to inconsistencies between the flux calculation and the change in the area of a cell. Our code is publicly available as open source and designed in an object-oriented, user-friendly way that facilitates incorporation of new algorithms and physical processes.« less

Intercomparison of 3D pore-scale flow and solute transport simulation methods

DOE PAGES

Mehmani, Yashar; Schoenherr, Martin; Pasquali, Andrea; ...

2015-09-28

Multiple numerical approaches have been developed to simulate porous media fluid flow and solute transport at the pore scale. These include 1) methods that explicitly model the three-dimensional geometry of pore spaces and 2) methods that conceptualize the pore space as a topologically consistent set of stylized pore bodies and pore throats. In previous work we validated a model of the first type, using computational fluid dynamics (CFD) codes employing a standard finite volume method (FVM), against magnetic resonance velocimetry (MRV) measurements of pore-scale velocities. Here we expand that validation to include additional models of the first type based onmore » the lattice Boltzmann method (LBM) and smoothed particle hydrodynamics (SPH), as well as a model of the second type, a pore-network model (PNM). The PNM approach used in the current study was recently improved and demonstrated to accurately simulate solute transport in a two-dimensional experiment. While the PNM approach is computationally much less demanding than direct numerical simulation methods, the effect of conceptualizing complex three-dimensional pore geometries on solute transport in the manner of PNMs has not been fully determined. We apply all four approaches (FVM-based CFD, LBM, SPH and PNM) to simulate pore-scale velocity distributions and (for capable codes) nonreactive solute transport, and intercompare the model results. Comparisons are drawn both in terms of macroscopic variables (e.g., permeability, solute breakthrough curves) and microscopic variables (e.g., local velocities and concentrations). Generally good agreement was achieved among the various approaches, but some differences were observed depending on the model context. The intercomparison work was challenging because of variable capabilities of the codes, and inspired some code enhancements to allow consistent comparison of flow and transport simulations across the full suite of methods. This paper provides support for

Intercomparison of 3D pore-scale flow and solute transport simulation methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xiaofan; Mehmani, Yashar; Perkins, William A.

2016-09-01

Multiple numerical approaches have been developed to simulate porous media fluid flow and solute transport at the pore scale. These include 1) methods that explicitly model the three-dimensional geometry of pore spaces and 2) methods that conceptualize the pore space as a topologically consistent set of stylized pore bodies and pore throats. In previous work we validated a model of the first type, using computational fluid dynamics (CFD) codes employing a standard finite volume method (FVM), against magnetic resonance velocimetry (MRV) measurements of pore-scale velocities. Here we expand that validation to include additional models of the first type based onmore » the lattice Boltzmann method (LBM) and smoothed particle hydrodynamics (SPH), as well as a model of the second type, a pore-network model (PNM). The PNM approach used in the current study was recently improved and demonstrated to accurately simulate solute transport in a two-dimensional experiment. While the PNM approach is computationally much less demanding than direct numerical simulation methods, the effect of conceptualizing complex three-dimensional pore geometries on solute transport in the manner of PNMs has not been fully determined. We apply all four approaches (FVM-based CFD, LBM, SPH and PNM) to simulate pore-scale velocity distributions and (for capable codes) nonreactive solute transport, and intercompare the model results. Comparisons are drawn both in terms of macroscopic variables (e.g., permeability, solute breakthrough curves) and microscopic variables (e.g., local velocities and concentrations). Generally good agreement was achieved among the various approaches, but some differences were observed depending on the model context. The intercomparison work was challenging because of variable capabilities of the codes, and inspired some code enhancements to allow consistent comparison of flow and transport simulations across the full suite of methods. This study provides support for

Variable stars in Local Group Galaxies - II. Sculptor dSph

NASA Astrophysics Data System (ADS)

Martínez-Vázquez, C. E.; Stetson, P. B.; Monelli, M.; Bernard, E. J.; Fiorentino, G.; Gallart, C.; Bono, G.; Cassisi, S.; Dall'Ora, M.; Ferraro, I.; Iannicola, G.; Walker, A. R.

2016-11-01

We present the identification of 634 variable stars in the Milky Way dwarf spheroidal (dSph) satellite Sculptor based on archival ground-based optical observations spanning ˜24 yr and covering ˜2.5 deg2. We employed the same methodologies as the `Homogeneous Photometry' series published by Stetson. In particular, we have identified and characterized one of the largest (536) RR Lyrae samples so far in a Milky Way dSph satellite. We have also detected four Anomalous Cepheids, 23 SX Phoenicis stars, five eclipsing binaries, three field variable stars, three peculiar variable stars located above the horizontal branch - near to the locus of BL Herculis - that we are unable to classify properly. Additionally, we identify 37 long period variables plus 23 probable variable stars, for which the current data do not allow us to determine the period. We report positions and finding charts for all the variable stars, and basic properties (period, amplitude, mean magnitude) and light curves for 574 of them. We discuss the properties of the RR Lyrae stars in the Bailey diagram, which supports the coexistence of subpopulations with different chemical compositions. We estimate the mean mass of Anomalous Cepheids (˜1.5 M⊙) and SX Phoenicis stars (˜1 M⊙). We discuss in detail the nature of the former. The connections between the properties of the different families of variable stars are discussed in the context of the star formation history of the Sculptor dSph galaxy.

A fully coupled 3D transport model in SPH for multi-species reaction-diffusion systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adami, Stefan; Hu, X. Y.; Adams, N. A.

2011-08-23

Abstract—In this paper we present a fully generalized transport model for multiple species in complex two and threedimensional geometries. Based on previous work [1] we have extended our interfacial reaction-diffusion model to handle arbitrary numbers of species allowing for coupled reaction models. Each species is tracked independently and we consider different physics of a species with respect to the bulk phases in contact. We use our SPH model to simulate the reaction-diffusion problem on a pore-scale level of a solid oxide fuel cell (SOFC) with special emphasize on the effect of surface diffusion.

Comparisons of Simulated Hydrodynamics and Water Quality for Projected Demands in 2046, Pueblo Reservoir, Southeastern Colorado

USGS Publications Warehouse

Ortiz, Roderick F.; Galloway, Joel M.; Miller, Lisa D.; Mau, David P.

2008-01-01

Pueblo Reservoir is one of southeastern Colorado's most valuable water resources. The reservoir provides irrigation, municipal, and industrial water to various entities throughout the region. The reservoir also provides flood control, recreational activities, sport fishing, and wildlife enhancement to the region. The Bureau of Reclamation is working to meet its goal to issue a Final Environmental Impact Statement (EIS) on the Southern Delivery System project (SDS). SDS is a regional water-delivery project that has been proposed to provide a safe, reliable, and sustainable water supply through the foreseeable future (2046) for Colorado Springs, Fountain, Security, and Pueblo West. Discussions with the Bureau of Reclamation and the U.S. Geological Survey led to a cooperative agreement to simulate the hydrodynamics and water quality of Pueblo Reservoir. This work has been completed and described in a previously published report, U.S. Geological Survey Scientific Investigations Report 2008-5056. Additionally, there was a need to make comparisons of simulated hydrodynamics and water quality for projected demands associated with the various EIS alternatives and plans by Pueblo West to discharge treated water into the reservoir. Plans by Pueblo West are fully independent of the SDS project. This report compares simulated hydrodynamics and water quality for projected demands in Pueblo Reservoir resulting from changes in inflow and water quality entering the reservoir, and from changes to withdrawals from the reservoir as projected for the year 2046. Four of the seven EIS alternatives were selected for scenario simulations. The four U.S. Geological Survey simulation scenarios were the No Action scenario (EIS Alternative 1), the Downstream Diversion scenario (EIS Alternative 2), the Upstream Return-Flow scenario (EIS Alternative 4), and the Upstream Diversion scenario (EIS Alternative 7). Additionally, the results of an Existing Conditions scenario (water years 2000 through

GRADSPMHD: A parallel MHD code based on the SPH formalism

NASA Astrophysics Data System (ADS)

Vanaverbeke, S.; Keppens, R.; Poedts, S.

2014-03-01

We present GRADSPMHD, a completely Lagrangian parallel magnetohydrodynamics code based on the SPH formalism. The implementation of the equations of SPMHD in the “GRAD-h” formalism assembles known results, including the derivation of the discretized MHD equations from a variational principle, the inclusion of time-dependent artificial viscosity, resistivity and conductivity terms, as well as the inclusion of a mixed hyperbolic/parabolic correction scheme for satisfying the ∇ṡB→ constraint on the magnetic field. The code uses a tree-based formalism for neighbor finding and can optionally use the tree code for computing the self-gravity of the plasma. The structure of the code closely follows the framework of our parallel GRADSPH FORTRAN 90 code which we added previously to the CPC program library. We demonstrate the capabilities of GRADSPMHD by running 1, 2, and 3 dimensional standard benchmark tests and we find good agreement with previous work done by other researchers. The code is also applied to the problem of simulating the magnetorotational instability in 2.5D shearing box tests as well as in global simulations of magnetized accretion disks. We find good agreement with available results on this subject in the literature. Finally, we discuss the performance of the code on a parallel supercomputer with distributed memory architecture. Catalogue identifier: AERP_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AERP_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 620503 No. of bytes in distributed program, including test data, etc.: 19837671 Distribution format: tar.gz Programming language: FORTRAN 90/MPI. Computer: HPC cluster. Operating system: Unix. Has the code been vectorized or parallelized?: Yes, parallelized using MPI. RAM: ˜30 MB for a

Draft Genome Sequence of Methylovulum psychrotolerans Sph1T, an Obligate Methanotroph from Low-Temperature Environments.

PubMed

Oshkin, Igor Y; Miroshnikov, Kirill K; Belova, Svetlana E; Korzhenkov, Aleksei A; Toshchakov, Stepan V; Dedysh, Svetlana N

2018-03-15

Methylovulum psychrotolerans Sph1 T is an aerobic, obligate methanotroph, which was isolated from cold methane seeps in West Siberia. This bacterium possesses only a particulate methane monooxygenase and is widely distributed in low-temperature environments. Strain Sph1 T has the genomic potential for biosynthesis of hopanoids required for the maintenance of intracytoplasmic membranes. Copyright © 2018 Oshkin et al.

A Test Suite for 3D Radiative Hydrodynamics Simulations of Protoplanetary Disks

NASA Astrophysics Data System (ADS)

Boley, Aaron C.; Durisen, R. H.; Nordlund, A.; Lord, J.

2006-12-01

Radiative hydrodynamics simulations of protoplanetary disks with different treatments for radiative cooling demonstrate disparate evolutions (see Durisen et al. 2006, PPV chapter). Some of these differences include the effects of convection and metallicity on disk cooling and the susceptibility of the disk to fragmentation. Because a principal reason for these differences may be the treatment of radiative cooling, the accuracy of cooling algorithms must be evaluated. In this paper we describe a radiative transport test suite, and we challenge all researchers who use radiative hydrodynamics to study protoplanetary disk evolution to evaluate their algorithms with these tests. The test suite can be used to demonstrate an algorithm's accuracy in transporting the correct flux through an atmosphere and in reaching the correct temperature structure, to test the algorithm's dependence on resolution, and to determine whether the algorithm permits of inhibits convection when expected. In addition, we use this test suite to demonstrate the accuracy of a newly developed radiative cooling algorithm that combines vertical rays with flux-limited diffusion. This research was supported in part by a Graduate Student Researchers Program fellowship.

Construction, MD simulation, and hydrodynamic validation of an all-atom model of a monoclonal IgG antibody.

PubMed

Brandt, J Paul; Patapoff, Thomas W; Aragon, Sergio R

2010-08-04

At 150 kDa, antibodies of the IgG class are too large for their structure to be determined with current NMR methodologies. Because of hinge-region flexibility, it is difficult to obtain atomic-level structural information from the crystal, and questions regarding antibody structure and dynamics in solution remain unaddressed. Here we describe the construction of a model of a human IgG1 monoclonal antibody (trastuzumab) from the crystal structures of fragments. We use a combination of molecular-dynamics (MD) simulation, continuum hydrodynamics modeling, and experimental diffusion measurements to explore antibody behavior in aqueous solution. Hydrodynamic modeling provides a link between the atomic-level details of MD simulation and the size- and shape-dependent data provided by hydrodynamic measurements. Eight independent 40 ns MD trajectories were obtained with the AMBER program suite. The ensemble average of the computed transport properties over all of the MD trajectories agrees remarkably well with the value of the translational diffusion coefficient obtained with dynamic light scattering at 20 degrees C and 27 degrees C, and the intrinsic viscosity measured at 20 degrees C. Therefore, our MD results likely represent a realistic sampling of the conformational space that an antibody explores in aqueous solution. 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Modeling Water Waves with Smoothed Particle Hydrodynamics

DTIC Science & Technology

2013-09-30

SPH Model for Water Waves and Other Free Surface Flows ...Lagrangian nature of SPH allows the modeling of wave breaking, surf zones, ship waves, and wave-structure interaction, where the free surface becomes...proving to be a competent modeling scheme for free surface flows in three dimensions including the complex flows of the surf zone. As the GPU

A hybrid model for coupling kinetic corrections of fusion reactivity to hydrodynamic implosion simulations

NASA Astrophysics Data System (ADS)

Tang, Xian-Zhu; McDevitt, C. J.; Guo, Zehua; Berk, H. L.

2014-03-01

Inertial confinement fusion requires an imploded target in which a central hot spot is surrounded by a cold and dense pusher. The hot spot/pusher interface can take complicated shape in three dimensions due to hydrodynamic mix. It is also a transition region where the Knudsen and inverse Knudsen layer effect can significantly modify the fusion reactivity in comparison with the commonly used value evaluated with background Maxwellians. Here, we describe a hybrid model that couples the kinetic correction of fusion reactivity to global hydrodynamic implosion simulations. The key ingredient is a non-perturbative treatment of the tail ions in the interface region where the Gamow ion Knudsen number approaches or surpasses order unity. The accuracy of the coupling scheme is controlled by the precise criteria for matching the non-perturbative kinetic model to perturbative solutions in both configuration space and velocity space.

Rapid Optimal SPH Particle Distributions in Spherical Geometries For Creating Astrophysical Initial Conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Raskin, Cody; Owen, J. Michael

Creating spherical initial conditions in smoothed particle hydrodynamics simulations that are spherically conformal is a difficult task. Here in this paper, we describe two algorithmic methods for evenly distributing points on surfaces that when paired can be used to build three-dimensional spherical objects with optimal equipartition of volume between particles, commensurate with an arbitrary radial density function. We demonstrate the efficacy of our method against stretched lattice arrangements on the metrics of hydrodynamic stability, spherical conformity, and the harmonic power distribution of gravitational settling oscillations. We further demonstrate how our method is highly optimized for simulating multi-material spheres, such asmore » planets with core–mantle boundaries.« less

Rapid Optimal SPH Particle Distributions in Spherical Geometries For Creating Astrophysical Initial Conditions

DOE PAGES

Raskin, Cody; Owen, J. Michael

2016-03-24

Creating spherical initial conditions in smoothed particle hydrodynamics simulations that are spherically conformal is a difficult task. Here in this paper, we describe two algorithmic methods for evenly distributing points on surfaces that when paired can be used to build three-dimensional spherical objects with optimal equipartition of volume between particles, commensurate with an arbitrary radial density function. We demonstrate the efficacy of our method against stretched lattice arrangements on the metrics of hydrodynamic stability, spherical conformity, and the harmonic power distribution of gravitational settling oscillations. We further demonstrate how our method is highly optimized for simulating multi-material spheres, such asmore » planets with core–mantle boundaries.« less

Investigating mass transfer in symbiotic systems with hydrodynamic simulations

NASA Astrophysics Data System (ADS)

de Val-Borro, Miguel; Karovska, Margarita; Sasselov, Dimitar D.

2014-06-01

We investigate gravitationally focused wind accretion in binary systems consisting of an evolved star with a gaseous envelope and a compact accreting companion. We study the mass accretion and formation of an accretion disk around the secondary caused by the strong wind from the primary late-type component using global 2D and 3D hydrodynamic numerical simulations. In particular, the dependence on the mass accretion rate on the mass loss rate, wind temperature and orbital parameters of the system is considered. For a typical slow and massive wind from an evolved star the mass transfer through a focused wind results in rapid infall onto the secondary. A stream flow is created between the stars with accretion rates of a 2-10% percent of the mass loss from the primary. This mechanism could be an important method for explaining periodic modulations in the accretion rates for a broad range of interacting binary systems and fueling of a large population of X-ray binary systems. We test the plausibility of these accretion flows indicated by the simulations by comparing with observations of the symbiotic CH Cyg variable system.

Stochastic simulation of reaction-diffusion systems: A fluctuating-hydrodynamics approach

DOE PAGES

Kim, Changho; Nonaka, Andy; Bell, John B.; ...

2017-03-24

Here, we develop numerical methods for stochastic reaction-diffusion systems based on approaches used for fluctuating hydrodynamics (FHD). For hydrodynamic systems, the FHD formulation is formally described by stochastic partial differential equations (SPDEs). In the reaction-diffusion systems we consider, our model becomes similar to the reaction-diffusion master equation (RDME) description when our SPDEs are spatially discretized and reactions are modeled as a source term having Poisson fluctuations. However, unlike the RDME, which becomes prohibitively expensive for an increasing number of molecules, our FHD-based description naturally extends from the regime where fluctuations are strong, i.e., each mesoscopic cell has few (reactive) molecules,more » to regimes with moderate or weak fluctuations, and ultimately to the deterministic limit. By treating diffusion implicitly, we avoid the severe restriction on time step size that limits all methods based on explicit treatments of diffusion and construct numerical methods that are more efficient than RDME methods, without compromising accuracy. Guided by an analysis of the accuracy of the distribution of steady-state fluctuations for the linearized reaction-diffusion model, we construct several two-stage (predictor-corrector) schemes, where diffusion is treated using a stochastic Crank-Nicolson method, and reactions are handled by the stochastic simulation algorithm of Gillespie or a weakly second-order tau leaping method. We find that an implicit midpoint tau leaping scheme attains second-order weak accuracy in the linearized setting and gives an accurate and stable structure factor for a time step size of an order of magnitude larger than the hopping time scale of diffusing molecules. We study the numerical accuracy of our methods for the Schlögl reaction-diffusion model both in and out of thermodynamic equilibrium. We demonstrate and quantify the importance of thermodynamic fluctuations to the formation of a

A clip-domain serine proteinase homolog (SPH) in oriental river prawn, Macrobrachium nipponense provides insights into its role in innate immune response.

PubMed

Ding, Zhili; Kong, Youqin; Chen, Liqiao; Qin, Jianguang; Sun, Shengming; Li, Ming; Du, Zhenyu; Ye, Jinyun

2014-08-01

In this study, a clip-domain serine proteinase homolog designated as MnSPH was cloned and characterized from a freshwater prawn Macrobrachium nipponense. The full-length cDNA of MnSPH was 1897 bp and contained a 1701 bp open reading frame (ORF) encoding a protein of 566 amino acids, a 103 bp 5'-untranslated region, and a 93 bp 3'-untranslated region. Sequence comparison showed that the deduced amino acids of MnSPH shared 30-59% identity with sequences reported in other animals. Tissue distribution analysis indicated that the MnSPH transcripts were present in all detected tissues with highest in the hepatopancreas and ovary. The MnSPH mRNA levels in the developing ovary were stable at the initial three developmental stages, then increased gradually from stage IV (later vitellogenesis), and reached a maximum at stage VI (paracmasis). Furthermore, the expression of MnSPH mRNA in hemocytes was significantly up-regulated at 1.5 h, 6 h, 12 h and 48 h post Aeromonas hydrophila injection. The increased phenoloxidase activity also demonstrated a clear time-dependent pattern after A. hydrophila challenge. These results suggest that MnSPH participates in resisting to pathogenic microorganisms and plays a pivotal role in host defense against microbe invasion in M. nipponense. Copyright © 2014 Elsevier Ltd. All rights reserved.

Hydrodynamic modeling of petroleum reservoirs using simulator MUFITS

NASA Astrophysics Data System (ADS)

Afanasyev, Andrey

2015-04-01

MUFITS is new noncommercial software for numerical modeling of subsurface processes in various applications (www.mufits.imec.msu.ru). To this point, the simulator was used for modeling nonisothermal flows in geothermal reservoirs and for modeling underground carbon dioxide storage. In this work, we present recent extension of the code to petroleum reservoirs. The simulator can be applied in conventional black oil modeling, but it also utilizes a more complicated models for volatile oil and gas condensate reservoirs as well as for oil rim fields. We give a brief overview of the code by providing the description of internal representation of reservoir models, which are constructed of grid blocks, interfaces, stock tanks as well as of pipe segments and pipe junctions for modeling wells and surface networks. For conventional black oil approach, we present the simulation results for SPE comparative tests. We propose an accelerated compositional modeling method for sub- and supercritical flows subjected to various phase equilibria, particularly to three-phase equilibria of vapour-liquid-liquid type. The method is based on the calculation of the thermodynamic potential of reservoir fluid as a function of pressure, total enthalpy and total composition and storing its values as a spline table, which is used in hydrodynamic simulation for accelerated PVT properties prediction. We provide the description of both the spline calculation procedure and the flashing algorithm. We evaluate the thermodynamic potential for a mixture of two pseudo-components modeling the heavy and light hydrocarbon fractions. We develop a technique for converting black oil PVT tables to the potential, which can be used for in-situ hydrocarbons multiphase equilibria prediction under sub- and supercritical conditions, particularly, in gas condensate and volatile oil reservoirs. We simulate recovery from a reservoir subject to near-critical initial conditions for hydrocarbon mixture. We acknowledge

Dark matter in the Reticulum II dSph: a radio search

NASA Astrophysics Data System (ADS)

Regis, Marco; Richter, Laura; Colafrancesco, Sergio

2017-07-01

We present a deep radio search in the Reticulum II dwarf spheroidal (dSph) galaxy performed with the Australia Telescope Compact Array. Observations were conducted at 16 cm wavelength, with an rms sensitivity of 0.01 mJy/beam, and with the goal of searching for synchrotron emission induced by annihilation or decay of weakly interacting massive particles (WIMPs). Data were complemented with observations on large angular scales taken with the KAT-7 telescope. We find no evidence for a diffuse emission from the dSph and we derive competitive bounds on the WIMP properties. In addition, we detect more than 200 new background radio sources. Among them, we show there are two compelling candidates for being the radio counterpart of the possible γ-ray emission reported by other groups using Fermi-LAT data.

Numerical Hydrodynamics in Special Relativity.

PubMed

Martí, José Maria; Müller, Ewald

2003-01-01

This review is concerned with a discussion of numerical methods for the solution of the equations of special relativistic hydrodynamics (SRHD). Particular emphasis is put on a comprehensive review of the application of high-resolution shock-capturing methods in SRHD. Results of a set of demanding test bench simulations obtained with different numerical SRHD methods are compared. Three applications (astrophysical jets, gamma-ray bursts and heavy ion collisions) of relativistic flows are discussed. An evaluation of various SRHD methods is presented, and future developments in SRHD are analyzed involving extension to general relativistic hydrodynamics and relativistic magneto-hydrodynamics. The review further provides FORTRAN programs to compute the exact solution of a 1D relativistic Riemann problem with zero and nonzero tangential velocities, and to simulate 1D relativistic flows in Cartesian Eulerian coordinates using the exact SRHD Riemann solver and PPM reconstruction. Supplementary material is available for this article at 10.12942/lrr-2003-7 and is accessible for authorized users.

Hydrodynamical and Spectral Simulations of HMXB Winds

NASA Astrophysics Data System (ADS)

Mauche, Christopher W.; Liedahl, D. A.; Plewa, T.

2006-09-01

We describe the results of a research program to develop improved models of the X-ray spectra of cosmic sources such as X-ray binaries, CVs, and AGN in which UV line-driven mass flows are photoionized by an X-ray source. Work to date has focused on high-mass X-ray binaries (HMXBs) and on Vela X-1 in particular, for which there are high-quality Chandra HETG spectra in the archive. Our research program combines FLASH hydrodynamic calculations, XSTAR photoionization calculations, HULLAC atomic data, improved calculations of the line force multiplier, X-ray emission models appropriate to X-ray photoionized plasmas, and Monte Carlo radiation transport. We will present movies of the relevant physical quantities (density, temperature, ionization parameter, velocity) from a FLASH two-dimensional time-dependent simulation of Vela X-1, maps showing the emissivity distributions of the X-ray emission lines, and a preliminary comparison of the resulting synthetic spectra to the Chandra HETG spectra. This work was performed under the auspices of the U.S. Department of Energy by University of California, Lawrence Livermore National Laboratory under Contract W-7405-Eng-48.

Revised Comparisons of Simulated Hydrodynamics and Water Quality for Projected Demands in 2046, Pueblo Reservoir, Southeastern Colorado

USGS Publications Warehouse

Ortiz, Roderick F.; Miller, Lisa D.

2009-01-01

Pueblo Reservoir is one of southeastern Colorado's most valuable water resources. The reservoir provides irrigation, municipal, and industrial water to various entities throughout the region. The reservoir also provides flood control, recreational activities, sport fishing, and wildlife enhancement to the region. The Southern Delivery System (SDS) project is a regional water-delivery project that has been proposed to provide a safe, reliable, and sustainable water supply through the foreseeable future (2046) for Colorado Springs, Fountain, Security, and Pueblo West. Discussions with the Bureau of Reclamation and the U.S. Geological Survey led to a cooperative agreement to simulate the hydrodynamics and water quality of Pueblo Reservoir. This work has been completed and described in a previously published report, U.S. Geological Survey Scientific Investigations Report 2008-5056. Additionally, there was a need to make comparisons of simulated hydrodynamics and water quality for projected demands associated with the various Environmental Impact Statements (EIS) alternatives and plans by Pueblo West to discharge treated wastewater into the reservoir. Wastewater plans by Pueblo West are fully independent of the SDS project. This report compares simulated hydrodynamics and water quality for projected demands in Pueblo Reservoir resulting from changes in inflow and water quality entering the reservoir, and from changes to withdrawals from the reservoir as projected for the year 2046. Four of the seven EIS alternatives were selected for scenario simulations. The four U.S. Geological Survey simulation scenarios were the No Action scenario (EIS Alternative 1), the Downstream Diversion scenario (EIS Alternative 2), the Upstream Return-Flow scenario (EIS Alternative 4), and the Upstream Diversion scenario (EIS Alternative 7). Additionally, the results of an Existing Conditions scenario (year 2006 demand conditions) were compared to the No Action scenario (projected demands in

Viscous Overstability in Saturn's B-Ring. II. Hydrodynamic Theory and Comparison to Simulations

NASA Astrophysics Data System (ADS)

Schmidt, Jürgen; Salo, Heikki; Spahn, Frank; Petzschmann, Olaf

2001-10-01

We investigate the viscous oscillatory instability (overstability) of an unperturbed dense planetary ring, an instability that might play a role in the formation of radial structure in Saturn's B-ring. We generalize existing hydrodynamic models by including the heat flow equation in the analysis and compare our results to the development of overstable modes in local particle simulations. With the heat flow, in addition to the balance equations for mass and momentum, we take into account the balance law for the energy of the random motion; i.e., we allow for a thermal mode in a stability analysis of the stationary Keplerian flow. We also incorporate the effects of nonlocal transport of momentum and energy on the stability of the ring. In a companion paper (Salo, H., J. Schmidt, and F. Spahn 2001. Icarus, doi:10.1006/icar.2001.6680) we describe the determination of the local and nonlocal parts of the viscosity, the heat conductivity, the pressure, as well as the collisional cooling, together with their dependences on temperature and density, in local event-driven simulations of a planetary ring. The ring's self-gravity is taken into account in these simulations by an enhancement of the frequency of vertical oscillations Ω z>Ω. We use these values as parameters in our hydrodynamic model for the comparison to overstability in simulated rings of meter-sized inelastic particles of large optical depth with Ω z/Ω=3.6. We find that the inclusion of the energy-balance equation has a stabilizing influence on the overstable modes, shifting the stability boundary to higher optical depths, and moderating the growth rates of the instability, as compared to a purely isothermal treatment. The non-isothermal model predicts correctly the growth rates and oscillation frequencies of overstable modes in the simulations, as well as the phase shifts and relative amplitudes of the perturbations in density and radial and tangential velocity.

Constraining the Properties of the Eta Carinae System via 3-D SPH Models of Space-Based Observations: The Absolute Orientation of the Binary Orbit

NASA Technical Reports Server (NTRS)

Madura, Thomas I.; Gull, Theodore R.; Owocki, Stanley P.; Okazaki, Atsuo T.; Russell, Christopher M. P.

2011-01-01

The extremely massive (> 90 Stellar Mass) and luminous (= 5 x 10(exp 6) Stellar Luminosity) star Eta Carinae, with its spectacular bipolar "Homunculus" nebula, comprises one of the most remarkable and intensely observed stellar systems in the Galaxy. However, many of its underlying physical parameters remain unknown. Multiwavelength variations observed to occur every 5.54 years are interpreted as being due to the collision of a massive wind from the primary star with the fast, less dense wind of a hot companion star in a highly elliptical (e approx. 0.9) orbit. Using three-dimensional (3-D) Smoothed Particle Hydrodynamics (SPH) simulations of the binary wind-wind collision, together with radiative transfer codes, we compute synthetic spectral images of [Fe III] emission line structures and compare them to existing Hubble Space Telescope/Space Telescope Imaging Spectrograph (HST/STIS) observations. We are thus able, for the first time, to tightly constrain the absolute orientation of the binary orbit on the sky. An orbit with an inclination of approx. 40deg, an argument of periapsis omega approx. 255deg, and a projected orbital axis with a position angle of approx. 312deg east of north provides the best fit to the observations, implying that the orbital axis is closely aligned in 3-D space with the Homunculus symmetry axis, and that the companion star orbits clockwise on the sky relative to the primary.

Super-rogue waves in simulations based on weakly nonlinear and fully nonlinear hydrodynamic equations.

PubMed

Slunyaev, A; Pelinovsky, E; Sergeeva, A; Chabchoub, A; Hoffmann, N; Onorato, M; Akhmediev, N

2013-07-01

The rogue wave solutions (rational multibreathers) of the nonlinear Schrödinger equation (NLS) are tested in numerical simulations of weakly nonlinear and fully nonlinear hydrodynamic equations. Only the lowest order solutions from 1 to 5 are considered. A higher accuracy of wave propagation in space is reached using the modified NLS equation, also known as the Dysthe equation. This numerical modeling allowed us to directly compare simulations with recent results of laboratory measurements in Chabchoub et al. [Phys. Rev. E 86, 056601 (2012)]. In order to achieve even higher physical accuracy, we employed fully nonlinear simulations of potential Euler equations. These simulations provided us with basic characteristics of long time evolution of rational solutions of the NLS equation in the case of near-breaking conditions. The analytic NLS solutions are found to describe the actual wave dynamics of steep waves reasonably well.

Hydrodynamic Simulation of the Cosmological X-Ray Background

NASA Astrophysics Data System (ADS)

Croft, Rupert A. C.; Di Matteo, Tiziana; Davé, Romeel; Hernquist, Lars; Katz, Neal; Fardal, Mark A.; Weinberg, David H.

2001-08-01

We use a hydrodynamic simulation of an inflationary cold dark matter model with a cosmological constant to predict properties of the extragalactic X-ray background (XRB). We focus on emission from the intergalactic medium (IGM), with particular attention to diffuse emission from warm-hot gas that lies in relatively smooth filamentary structures between galaxies and galaxy clusters. We also include X-rays from point sources associated with galaxies in the simulation, and we make maps of the angular distribution of the emission. Although much of the X-ray luminous gas has a filamentary structure, the filaments are not evident in the simulated maps because of projection effects. In the soft (0.5-2 keV) band, our calculated mean intensity of radiation from intergalactic and cluster gas is 2.3×10-12 ergs-1 cm-2 deg-2, 35% of the total softband emission. This intensity is compatible at the ~1 σ level with estimates of the unresolved soft background intensity from deep ROSAT and Chandra measurements. Only 4% of the hard (2-10 keV) emission is associated with intergalactic gas. Relative to active galactic nuclei flux, the IGM component of the XRB peaks at a lower redshift (median z~0.45) and spans a narrower redshift range, so its clustering makes an important contribution to the angular correlation function of the total emission. The clustering on the scales accessible to our simulation (0.1‧-10') is significant, with an amplitude roughly consistent with an extrapolation of recent ROSAT results to small scales. A cross-correlation analysis of the XRB against nearby galaxies taken from a simulated redshift survey also yields a strong signal from the IGM. Our conclusions about the soft background intensity differ from those of some recent papers that have argued that the expected emission from gas in galaxy, group, and cluster halos would exceed the observed background unless much of the gas is expelled by supernova feedback. We obtain reasonable compatibility with

Atomistic Simulations of Hydrodynamic and Interaction Forces on Functionalized Silica Nanoparticles

NASA Astrophysics Data System (ADS)

Lane, J. Matthew D.; Ismail, Ahmed E.; Chandross, Michael; Lorenz, Christian D.; Grest, Gary S.

2009-03-01

It is often desired to prevent the flocculation and phase separation of nanoparticles in solution. This can be accomplished either by manipulating the solvent or by tailoring the surface chemistry of the nanoparticles through functionalization with a monolayer of oligomer chains. Since it is not known how these functionalized coatings affect the interactions between nanoparticles and with the surrounding solvent, we present results from a series of molecular dynamics simulations of polyethylene oxide (PEO) coated silica nanoparticles of varying size (5 to 20 nm diameter) in water. For a single nanoparticle we determined the Stokes drag on the nanoparticle as it moves through the solvent and as it approaches a wall. Due to hydrodynamic interactions there are large finite size effects which we estimate by varying the size of the simulation cell. We also determined both solvent-mediated (velocity-independent) and lubrication (velocity-dependent) forces between two nanoparticles as a function of the coverage and chain length of the PEO chains.

Element fracture technique for hypervelocity impact simulation

NASA Astrophysics Data System (ADS)

Zhang, Xiao-tian; Li, Xiao-gang; Liu, Tao; Jia, Guang-hui

2015-05-01

Hypervelocity impact dynamics is the theoretical support of spacecraft shielding against space debris. The numerical simulation has become an important approach for obtaining the ballistic limits of the spacecraft shields. Currently, the most widely used algorithm for hypervelocity impact is the smoothed particle hydrodynamics (SPH). Although the finite element method (FEM) is widely used in fracture mechanics and low-velocity impacts, the standard FEM can hardly simulate the debris cloud generated by hypervelocity impact. This paper presents a successful application of the node-separation technique for hypervelocity impact debris cloud simulation. The node-separation technique assigns individual/coincident nodes for the adjacent elements, and it applies constraints to the coincident node sets in the modeling step. In the explicit iteration, the cracks are generated by releasing the constrained node sets that meet the fracture criterion. Additionally, the distorted elements are identified from two aspects - self-piercing and phase change - and are deleted so that the constitutive computation can continue. FEM with the node-separation technique is used for thin-wall hypervelocity impact simulations. The internal structures of the debris cloud in the simulation output are compared with that in the test X-ray graphs under different material fracture criteria. It shows that the pressure criterion is more appropriate for hypervelocity impact. The internal structures of the debris cloud are also simulated and compared under different thickness-to-diameter ratios (t/D). The simulation outputs show the same spall pattern with the tests. Finally, the triple-plate impact case is simulated with node-separation FEM.

Dark matter in the Reticulum II dSph: a radio search

DOE Office of Scientific and Technical Information (OSTI.GOV)

Regis, Marco; Richter, Laura; Colafrancesco, Sergio, E-mail: regis@to.infn.it, E-mail: llrichter@gmail.com, E-mail: sergio.colafrancesco@wits.ac.za

2017-07-01

We present a deep radio search in the Reticulum II dwarf spheroidal (dSph) galaxy performed with the Australia Telescope Compact Array. Observations were conducted at 16 cm wavelength, with an rms sensitivity of 0.01 mJy/beam, and with the goal of searching for synchrotron emission induced by annihilation or decay of weakly interacting massive particles (WIMPs). Data were complemented with observations on large angular scales taken with the KAT-7 telescope. We find no evidence for a diffuse emission from the dSph and we derive competitive bounds on the WIMP properties. In addition, we detect more than 200 new background radio sources.more » Among them, we show there are two compelling candidates for being the radio counterpart of the possible γ-ray emission reported by other groups using Fermi-LAT data.« less

A Novel Approach to Visualizing Dark Matter Simulations.

PubMed

Kaehler, R; Hahn, O; Abel, T

2012-12-01

In the last decades cosmological N-body dark matter simulations have enabled ab initio studies of the formation of structure in the Universe. Gravity amplified small density fluctuations generated shortly after the Big Bang, leading to the formation of galaxies in the cosmic web. These calculations have led to a growing demand for methods to analyze time-dependent particle based simulations. Rendering methods for such N-body simulation data usually employ some kind of splatting approach via point based rendering primitives and approximate the spatial distributions of physical quantities using kernel interpolation techniques, common in SPH (Smoothed Particle Hydrodynamics)-codes. This paper proposes three GPU-assisted rendering approaches, based on a new, more accurate method to compute the physical densities of dark matter simulation data. It uses full phase-space information to generate a tetrahedral tessellation of the computational domain, with mesh vertices defined by the simulation's dark matter particle positions. Over time the mesh is deformed by gravitational forces, causing the tetrahedral cells to warp and overlap. The new methods are well suited to visualize the cosmic web. In particular they preserve caustics, regions of high density that emerge, when several streams of dark matter particles share the same location in space, indicating the formation of structures like sheets, filaments and halos. We demonstrate the superior image quality of the new approaches in a comparison with three standard rendering techniques for N-body simulation data.

Numerical simulation of cerebrospinal fluid hydrodynamics in the healing process of hydrocephalus patients

NASA Astrophysics Data System (ADS)

Gholampour, S.; Fatouraee, N.; Seddighi, A. S.; Seddighi, A.

2017-05-01

Three-dimensional computational models of the cerebrospinal fluid (CSF) flow and brain tissue are presented for evaluation of their hydrodynamic conditions before and after shunting for seven patients with non-communicating hydrocephalus. One healthy subject is also modeled to compare deviated patients data to normal conditions. The fluid-solid interaction simulation shows the CSF mean pressure and pressure amplitude (the superior index for evaluation of non-communicating hydrocephalus) in patients at a greater point than those in the healthy subject by 5.3 and 2 times, respectively.

A Particle Model for Prediction of Cement Infiltration of Cancellous Bone in Osteoporotic Bone Augmentation.

PubMed

Basafa, Ehsan; Murphy, Ryan J; Kutzer, Michael D; Otake, Yoshito; Armand, Mehran

2013-01-01

Femoroplasty is a potential preventive treatment for osteoporotic hip fractures. It involves augmenting mechanical properties of the femur by injecting Polymethylmethacrylate (PMMA) bone cement. To reduce the risks involved and maximize the outcome, however, the procedure needs to be carefully planned and executed. An important part of the planning system is predicting infiltration of cement into the porous medium of cancellous bone. We used the method of Smoothed Particle Hydrodynamics (SPH) to model the flow of PMMA inside porous media. We modified the standard formulation of SPH to incorporate the extreme viscosities associated with bone cement. Darcy creeping flow of fluids through isotropic porous media was simulated and the results were compared with those reported in the literature. Further validation involved injecting PMMA cement inside porous foam blocks - osteoporotic cancellous bone surrogates - and simulating the injections using our proposed SPH model. Millimeter accuracy was obtained in comparing the simulated and actual cement shapes. Also, strong correlations were found between the simulated and the experimental data of spreading distance (R(2) = 0.86) and normalized pressure (R(2) = 0.90). Results suggest that the proposed model is suitable for use in an osteoporotic femoral augmentation planning framework.

Modeling the nanoscale viscoelasticity of fluids by bridging non-Markovian fluctuating hydrodynamics and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Voulgarakis, Nikolaos K.; Satish, Siddarth; Chu, Jhih-Wei

2009-12-01

A multiscale computational method is developed to model the nanoscale viscoelasticity of fluids by bridging non-Markovian fluctuating hydrodynamics (FHD) and molecular dynamics (MD) simulations. To capture the elastic responses that emerge at small length scales, we attach an additional rheological model parallel to the macroscopic constitutive equation of a fluid. The widely used linear Maxwell model is employed as a working choice; other models can be used as well. For a fluid that is Newtonian in the macroscopic limit, this approach results in a parallel Newtonian-Maxwell model. For water, argon, and an ionic liquid, the power spectrum of momentum field autocorrelation functions of the parallel Newtonian-Maxwell model agrees very well with those calculated from all-atom MD simulations. To incorporate thermal fluctuations, we generalize the equations of FHD to work with non-Markovian rheological models and colored noise. The fluctuating stress tensor (white noise) is integrated in time in the same manner as its dissipative counterpart and numerical simulations indicate that this approach accurately preserves the set temperature in a FHD simulation. By mapping position and velocity vectors in the molecular representation onto field variables, we bridge the non-Markovian FHD with atomistic MD simulations. Through this mapping, we quantitatively determine the transport coefficients of the parallel Newtonian-Maxwell model for water and argon from all-atom MD simulations. For both fluids, a significant enhancement in elastic responses is observed as the wave number of hydrodynamic modes is reduced to a few nanometers. The mapping from particle to field representations and the perturbative strategy of developing constitutive equations provide a useful framework for modeling the nanoscale viscoelasticity of fluids.

Hydrodynamics of an electrochemical membrane bioreactor.

PubMed

Wang, Ya-Zhou; Wang, Yun-Kun; He, Chuan-Shu; Yang, Hou-Yun; Sheng, Guo-Ping; Shen, Jin-You; Mu, Yang; Yu, Han-Qing

2015-05-22

An electrochemical membrane bioreactor (EMBR) has recently been developed for energy recovery and wastewater treatment. The hydrodynamics of the EMBR would significantly affect the mass transfers and reaction kinetics, exerting a pronounced effect on reactor performance. However, only scarce information is available to date. In this study, the hydrodynamic characteristics of the EMBR were investigated through various approaches. Tracer tests were adopted to generate residence time distribution curves at various hydraulic residence times, and three hydraulic models were developed to simulate the results of tracer studies. In addition, the detailed flow patterns of the EMBR were acquired from a computational fluid dynamics (CFD) simulation. Compared to the tank-in-series and axial dispersion ones, the Martin model could describe hydraulic performance of the EBMR better. CFD simulation results clearly indicated the existence of a preferential or circuitous flow in the EMBR. Moreover, the possible locations of dead zones in the EMBR were visualized through the CFD simulation. Based on these results, the relationship between the reactor performance and the hydrodynamics of EMBR was further elucidated relative to the current generation. The results of this study would benefit the design, operation and optimization of the EMBR for simultaneous energy recovery and wastewater treatment.

Hydrodynamics of an Electrochemical Membrane Bioreactor

PubMed Central

Wang, Ya-Zhou; Wang, Yun-Kun; He, Chuan-Shu; Yang, Hou-Yun; Sheng, Guo-Ping; Shen, Jin-You; Mu, Yang; Yu, Han-Qing

2015-01-01

An electrochemical membrane bioreactor (EMBR) has recently been developed for energy recovery and wastewater treatment. The hydrodynamics of the EMBR would significantly affect the mass transfers and reaction kinetics, exerting a pronounced effect on reactor performance. However, only scarce information is available to date. In this study, the hydrodynamic characteristics of the EMBR were investigated through various approaches. Tracer tests were adopted to generate residence time distribution curves at various hydraulic residence times, and three hydraulic models were developed to simulate the results of tracer studies. In addition, the detailed flow patterns of the EMBR were acquired from a computational fluid dynamics (CFD) simulation. Compared to the tank-in-series and axial dispersion ones, the Martin model could describe hydraulic performance of the EBMR better. CFD simulation results clearly indicated the existence of a preferential or circuitous flow in the EMBR. Moreover, the possible locations of dead zones in the EMBR were visualized through the CFD simulation. Based on these results, the relationship between the reactor performance and the hydrodynamics of EMBR was further elucidated relative to the current generation. The results of this study would benefit the design, operation and optimization of the EMBR for simultaneous energy recovery and wastewater treatment. PMID:25997399

Large-Scale Description of Interacting One-Dimensional Bose Gases: Generalized Hydrodynamics Supersedes Conventional Hydrodynamics

NASA Astrophysics Data System (ADS)

Doyon, Benjamin; Dubail, Jérôme; Konik, Robert; Yoshimura, Takato

2017-11-01

The theory of generalized hydrodynamics (GHD) was recently developed as a new tool for the study of inhomogeneous time evolution in many-body interacting systems with infinitely many conserved charges. In this Letter, we show that it supersedes the widely used conventional hydrodynamics (CHD) of one-dimensional Bose gases. We illustrate this by studying "nonlinear sound waves" emanating from initial density accumulations in the Lieb-Liniger model. We show that, at zero temperature and in the absence of shocks, GHD reduces to CHD, thus for the first time justifying its use from purely hydrodynamic principles. We show that sharp profiles, which appear in finite times in CHD, immediately dissolve into a higher hierarchy of reductions of GHD, with no sustained shock. CHD thereon fails to capture the correct hydrodynamics. We establish the correct hydrodynamic equations, which are finite-dimensional reductions of GHD characterized by multiple, disjoint Fermi seas. We further verify that at nonzero temperature, CHD fails at all nonzero times. Finally, we numerically confirm the emergence of hydrodynamics at zero temperature by comparing its predictions with a full quantum simulation performed using the NRG-TSA-abacus algorithm. The analysis is performed in the full interaction range, and is not restricted to either weak- or strong-repulsion regimes.

Hydrodynamic cavitation for sonochemical effects.

PubMed

Moholkar, V S; Kumar, P S; Pandit, A B

1999-03-01

A comparative study of hydrodynamic and acoustic cavitation has been made on the basis of numerical solutions of the Rayleigh-Plesset equation. The bubble/cavity behaviour has been studied under both acoustic and hydrodynamic cavitation conditions. The effect of varying pressure fields on the collapse of the cavity (sinusoidal for acoustic and linear for hydrodynamic) and also on the latter's dynamic behaviour has been studied. The variations of parameters such as initial cavity size, intensity of the acoustic field and irradiation frequency in the case of acoustic cavitation, and initial cavity size, final recovery pressure and time for pressure recovery in the case of hydrodynamic cavitation, have been found to have significant effects on cavity/bubble dynamics. The simulations reveal that the bubble/cavity collapsing behaviour in the case of hydrodynamic cavitation is accompanied by a large number of pressure pulses of relatively smaller magnitude, compared with just one or two pulses under acoustic cavitation. It has been shown that hydrodynamic cavitation offers greater control over operating parameters and the resultant cavitation intensity. Finally, a brief summary of the experimental results on the oxidation of aqueous KI solution with a hydrodynamic cavitation set-up is given which supports the conclusion of this numerical study. The methodology presented allows one to manipulate and optimise of specific process, either physical or chemical.

A model of mudflow propagation downstream from the Grohovo landslide near the city of Rijeka (Croatia)

NASA Astrophysics Data System (ADS)

Žic, E.; Arbanas, Ž.; Bićanić, N.; Ožanić, N.

2015-02-01

Mudflows regularly generate significant human and property losses. Analyzing mudflows is important to assess the risks and to delimit vulnerable areas where mitigation measures are required. The smoothed-particle hydrodynamics (SPH) model adopted here considers, in two phases, a granular skeleton with voids filled with either water or mud. The SPH depth-integrated numerical model (Pastor et al., 2009a) used for the present simulations is a 2-D model capable of predicting the runout distance, flow velocity, deposition pattern and the final volume of mudflows. It is based on mathematical and rheological models. In this study, the main characteristics of mudflow processes that have emerged in the past (1908) in the area downstream of the Grohovo landslide are examined, and the more relevant parameters and attributes describing the mudflow are presented. Principal equations that form the basis of the SPH depth-integrated model are reviewed and applied to analyze the Grohovo landslide and the propagation of the mudflow wave downstream of the landslide. Based on the SPH method, the runout distance, quantities of the deposited materials and the velocity of mudflow progression which occurred in the past at the observed area are analyzed and qualitatively compared to the recorded consequences of the actual event. Within the SPH simulation, the Newtonian rheological model in the turbulent flow regime and the Bingham rheological model were adopted and a comparison was made of the application of the Egashira and Hungr erosion law.

Radiation-hydrodynamic simulations of thermally-driven disc winds in X-ray binaries: A direct comparison to GRO J1655-40

NASA Astrophysics Data System (ADS)

Higginbottom, Nick; Knigge, Christian; Long, Knox S.; Matthews, James H.; Sim, Stuart A.; Hewitt, Henrietta A.

2018-06-01

Essentially all low-mass X-ray binaries (LMXBs) in the soft state appear to drive powerful equatorial disc winds. A simple mechanism for driving such outflows involves X-ray heating of the top of the disc atmosphere to the Compton temperature. Beyond the Compton radius, the thermal speed exceeds the escape velocity, and mass loss is inevitable. Here, we present the first coupled radiation-hydrodynamic simulation of such thermally-driven disc winds. The main advance over previous modelling efforts is that the frequency-dependent attenuation of the irradiating SED is taken into account. We can therefore relax the approximation that the wind is optically thin throughout which is unlikely to hold in the crucial acceleration zone of the flow. The main remaining limitations of our simulations are connected to our treatment of optically thick regions. Adopting parameters representative of the wind-driving LMXB GRO J1655-40, our radiation-hydrodynamic model yields a mass-loss rate that is ≃ 5 × lower than that suggested by pure hydrodynamic, optically thin models. This outflow rate still represents more than twice the accretion rate and agrees well with the mass-loss rate inferred from Chandra/HETG observations of GRO J1655-40 at a time when the system had a similar luminosity to that adopted in our simulations. The Fe XXV and Fe XXVI Lyman {α } absorption line profiles observed in this state are slightly stronger than those predicted by our simulations but the qualitative agreement between observed and simulated outflow properties means that thermal driving is a viable mechanism for powering the disc winds seen in soft-state LMXBs.

Simulation of river stage using artificial neural network and MIKE 11 hydrodynamic model

NASA Astrophysics Data System (ADS)

Panda, Rabindra K.; Pramanik, Niranjan; Bala, Biplab

2010-06-01

Simulation of water levels at different sections of a river using physically based flood routing models is quite cumbersome, because it requires many types of data such as hydrologic time series, river geometry, hydraulics of existing control structures and channel roughness coefficients. Normally in developing countries like India it is not easy to collect these data because of poor monitoring and record keeping. Therefore, an artificial neural network (ANN) technique is used as an effective alternative in hydrologic simulation studies. The present study aims at comparing the performance of the ANN technique with a widely used physically based hydrodynamic model in the MIKE 11 environment. The MIKE 11 hydrodynamic model was calibrated and validated for the monsoon periods (June-September) of the years 2006 and 2001, respectively. Feed forward neural network architecture with Levenberg-Marquardt (LM) back propagation training algorithm was used to train the neural network model using hourly water level data of the period June-September 2006. The trained ANN model was tested using data for the same period of the year 2001. Simulated water levels by the MIKE 11HD were compared with the corresponding water levels predicted by the ANN model. The results obtained from the ANN model were found to be much better than that of the MIKE 11HD results as indicated by the values of the goodness of fit indices used in the study. The Nash-Sutcliffe index ( E) and root mean square error (RMSE) obtained in case of the ANN model were found to be 0.8419 and 0.8939 m, respectively, during model testing, whereas in case of MIKE 11HD, the values of E and RMSE were found to be 0.7836 and 1.00 m, respectively, during model validation. The difference between the observed and simulated peak water levels obtained from the ANN model was found to be much lower than that of MIKE 11HD. The study reveals that the use of Levenberg-Marquardt algorithm with eight hidden neurons in the hidden layer

Differences in aquatic habitat quality as an impact of one- and two-dimensional hydrodynamic model simulated flow variables

NASA Astrophysics Data System (ADS)

Benjankar, R. M.; Sohrabi, M.; Tonina, D.; McKean, J. A.

2013-12-01

Aquatic habitat models utilize flow variables which may be predicted with one-dimensional (1D) or two-dimensional (2D) hydrodynamic models to simulate aquatic habitat quality. Studies focusing on the effects of hydrodynamic model dimensionality on predicted aquatic habitat quality are limited. Here we present the analysis of the impact of flow variables predicted with 1D and 2D hydrodynamic models on simulated spatial distribution of habitat quality and Weighted Usable Area (WUA) for fall-spawning Chinook salmon. Our study focuses on three river systems located in central Idaho (USA), which are a straight and pool-riffle reach (South Fork Boise River), small pool-riffle sinuous streams in a large meadow (Bear Valley Creek) and a steep-confined plane-bed stream with occasional deep forced pools (Deadwood River). We consider low and high flows in simple and complex morphologic reaches. Results show that 1D and 2D modeling approaches have effects on both the spatial distribution of the habitat and WUA for both discharge scenarios, but we did not find noticeable differences between complex and simple reaches. In general, the differences in WUA were small, but depended on stream type. Nevertheless, spatially distributed habitat quality difference is considerable in all streams. The steep-confined plane bed stream had larger differences between aquatic habitat quality defined with 1D and 2D flow models compared to results for streams with well defined macro-topographies, such as pool-riffle bed forms. KEY WORDS: one- and two-dimensional hydrodynamic models, habitat modeling, weighted usable area (WUA), hydraulic habitat suitability, high and low discharges, simple and complex reaches

Simulations of Model Microswimmers with Fully Resolved Hydrodynamics

NASA Astrophysics Data System (ADS)

Oyama, Norihiro; Molina, John J.; Yamamoto, Ryoichi

2017-10-01

Swimming microorganisms, which include bacteria, algae, and spermatozoa, play a fundamental role in most biological processes. These swimmers are a special type of active particle, that continuously convert local energy into propulsive forces, thereby allowing them to move through their surrounding fluid medium. While the size, shape, and propulsion mechanism vary from one organism to the next, they share certain general characteristics: they exhibit force-free motion and they swim at a small Reynolds number. To study the dynamics of such systems, we use the squirmer model, which provides an ideal representation of swimmers as spheroidal particles that propel owing to a modified boundary condition at their surface. We have considered the single-particle and many-particle dynamics of swimmers in bulk and confined systems using the smoothed profile method, which allows us to efficiently solve the coupled particle-fluid problem. For the single-particle dynamics, we studied the diffusive behavior caused by the swimming of the particles. At short-time scales, the diffusion is caused by the hydrodynamic interactions, whereas at long-time scales, it is determined by the particle-particle collisions. Thus, the short-time diffusion will be the same for both swimmers and inert tracer particles. We then investigated the dynamics of confined microswimmers using cylindrical and parallel-plate confining walls. For the cylindrical confinement, we find evidence of an order/disorder phase transition which depends on the specific type of swimmers and the size of the cylinder. Under parallel-plane walls, some swimmers exhibit wavelike modes, which lead to traveling density waves that bounce back and forth between the walls. From an analysis of the bulk systems, we can show that this wavelike motion can be understood as a pseudoacoustic mode and is a consequence of the intrinsic swimming properties of the particles. The results presented here, together with the simulation method that

The Sagittarius Dwarf Galaxy Survey (SDGS): Constraints on the Star Formation History of the Sgr dSph

NASA Astrophysics Data System (ADS)

Bellazzini, M.; Ferraro, F. R.; Buonanno, R.

1999-01-01

We present the first results of a large photometric survey devoted to the study of the star formation history in the Sagittarius dwarf spheroidal galaxy (Sgr dSph). Three large (size: 9 x 35 arcmin2) and widely spaced fields located nearly along the Sgr dSph major axis [(l,b) = (6.5 -16);(6-14);(5-12)] have been observed in the V and I passbands with the ESO-NTT 3.5-m telescope (La Silla - Chile). Well-calibrated photometry has been obtained for ˜90000 stars toward Sgr dSph and for ˜9000 stars in a (9 x 24 arcmin2) control field down to a limiting magnitude of V 22. At present this is the largest photometric (CCD) sample of Sgr dSph stars and the wide spacing between field provides the first opportunity of studying the stellar content of different regions of the galaxy (over a range of ˜2 Kpc across). Age and metallicity estimates are obtained for the detected stellar populations and the very first evidences are presented for (a) spatial differences in the stellar content and (b) the detection of a very metal poor population in the field of the Sgr galaxy.

Driving gas shells with radiation pressure on dust in radiation-hydrodynamic simulations

NASA Astrophysics Data System (ADS)

Costa, Tiago; Rosdahl, Joakim; Sijacki, Debora; Haehnelt, Martin G.

2018-01-01

We present radiation-hydrodynamic simulations of radiatively-driven gas shells launched by bright active galactic nuclei (AGN) in isolated dark matter haloes. Our goals are (1) to investigate the ability of AGN radiation pressure on dust to launch galactic outflows and (2) to constrain the efficiency of infrared (IR) multiscattering in boosting outflow acceleration. Our simulations are performed with the radiation-hydrodynamic code RAMSES-RT and include both single- and multiscattered radiation pressure from an AGN, radiative cooling and self-gravity. Since outflowing shells always eventually become transparent to the incident radiation field, outflows that sweep up all intervening gas are likely to remain gravitationally bound to their halo even at high AGN luminosities. The expansion of outflowing shells is well described by simple analytic models as long as the shells are mildly optically thick to IR radiation. In this case, an enhancement in the acceleration of shells through IR multiscattering occurs as predicted, i.e. a force \\dot{P} ≈ τ_IR L/c is exerted on the gas. For high optical depths τIR ≳ 50, however, momentum transfer between outflowing optically thick gas and IR radiation is rapidly suppressed, even if the radiation is efficiently confined. At high τIR, the characteristic flow time becomes shorter than the required trapping time of IR radiation such that the momentum flux \\dot{P} ≪ τ_IR L/c. We argue that while unlikely to unbind massive galactic gaseous haloes, AGN radiation pressure on dust could play an important role in regulating star formation and black hole accretion in the nuclei of massive compact galaxies at high redshift.

Effective dynamical coupling of hydrodynamics and transport for heavy-ion collisions

NASA Astrophysics Data System (ADS)

Oliinychenko, Dmytro; Petersen, Hannah

2017-04-01

Present hydrodynamics-based simulations of heavy-ion collisions neglect the feedback from the frozen-out particles flying back into the hydrodynamical region. This causes an artefact called “negative Cooper-Frye contributions”, which is negligible for high collision energies, but becomes significant for lower RHIC BES energies and for event-by-event simulations. To avoid negative Cooper-Frye contributions, while still preserving hydrodynamical behavior, we propose a pure hadronic transport approach with forced thermalization in the regions of high energy density. It is demonstrated that this approach exhibits enhancement of strangeness and mean transverse momenta compared to conventional transport - an effect typical for hydrodynamical approaches.

AX-GADGET: a new code for cosmological simulations of Fuzzy Dark Matter and Axion models

NASA Astrophysics Data System (ADS)

Nori, Matteo; Baldi, Marco

2018-05-01

We present a new module of the parallel N-Body code P-GADGET3 for cosmological simulations of light bosonic non-thermal dark matter, often referred as Fuzzy Dark Matter (FDM). The dynamics of the FDM features a highly non-linear Quantum Potential (QP) that suppresses the growth of structures at small scales. Most of the previous attempts of FDM simulations either evolved suppressed initial conditions, completely neglecting the dynamical effects of QP throughout cosmic evolution, or resorted to numerically challenging full-wave solvers. The code provides an interesting alternative, following the FDM evolution without impairing the overall performance. This is done by computing the QP acceleration through the Smoothed Particle Hydrodynamics (SPH) routines, with improved schemes to ensure precise and stable derivatives. As an extension of the P-GADGET3 code, it inherits all the additional physics modules implemented up to date, opening a wide range of possibilities to constrain FDM models and explore its degeneracies with other physical phenomena. Simulations are compared with analytical predictions and results of other codes, validating the QP as a crucial player in structure formation at small scales.

Simulating nanostorm heating in coronal loops using hydrodynamics and non-thermal particle evolution

NASA Astrophysics Data System (ADS)

Migliore, Christina; Winter, Henry; Murphy, Nicholas

2018-01-01

The solar corona is filled with loop-like structures that appear bright against the background when observed in the extreme ultraviolet (EUV). These loops have several remarkable properties that are not yet well understood. Warm loops (∼ 1 MK) appear to be ∼ 2 ‑ 9 times as dense at their apex as the predictions of hydrostatic atmosphere models. These loops also appear to be of constant cross-section despite the fact that the field strength in a potential magnetic field should decrease in the corona, causing the loops to expand. It is not clear why many active region loops appear to be of constant cross-section. Theories range from an internal twist of the magnetic field to observational effects. In this work we simulate active region loops heated by nanoflare storms using a dipolar magnetic field. We calculate the hydrodynamic properties for each loop using advanced hydrodynamics codes to simulate the corona and chromospheric response and basic dipole models to represent the magnetic fields of the loops. We show that even modest variations of the magnetic field strength along the loop can lead to drastic changes in the density profiles of active region loops, and they can also explain the overpressure at the apex of these loops. Synthetic AIA images of each loop are made to show the observable consequences of varying magnetic field strengths along the loop’s axis of symmetry. We also show how this work can lead to improved modeling of larger solar and stellar flares.

Rheology and hydrodynamic properties of Tolypocladium inflatum fermentation broth and its simulation.

PubMed

Benchapattarapong, N; Anderson, W A; Bai, F; Moo-Young, M

2005-07-01

A physico-chemical, two phase simulated pseudoplastic fermentation (SPF) broth was investigated in which Solka Floc cellulose fibre was used to simulate the filamentous biomass, and a mixture of 0.1% (w/v) carboxymethyl cellulose (CMC) and 0.15 M aqueous sodium chloride was used to simulate the liquid fraction of the fermentation broth. An investigation of the rheological behaviour and hydrodynamic properties of the SPF broth was carried out, and compared to both a fungal Tolypocladium inflatum fermentation broth and a CMC solution in a 50 L stirred tank bioreactor equipped with conventional Rushton turbines. The experimental data confirmed the ability of the two phase SPF broth to mimic both the T. inflatum broth bulk rheology as well as the mixing and mass transfer behaviour. In contrast, using a homogeneous CMC solution with a similar bulk rheology to simulate the fermentation resulted in a significant underestimation of the mass transfer and mixing times. The presence of the solid phase and its microstructure in the SPF broth appear to play a significant role in gas holdup and bubble size, thus leading to the different behaviours. The SPF broth seems to be a more accurate simulation fluid that can be used to predict the bioreactor mixing and mass transfer performance in filamentous fermentations, in comparison with CMC solutions used in some previous studies.

Co-assembly of Zn(SPh){sub 2} and organic linkers into helical and zig-zag polymer chains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu Yi; Yu Lingmin; Loo, Say Chye Joachim

2012-07-15

Two novel one-dimensional coordination polymers, single helicate [Zn(SPh){sub 2}(TPyTA)(EG)]{sub n} (EG=ethylene glycol) (1) and zig-zag structure [Zn(SPh){sub 2}(BPyVB)]{sub n} (2), were synthesized under solvothermal conditions at 150 Degree-Sign C or room temperature by the co-assembly of Zn(SPh){sub 2} and organic linkers such as 2,4,6-tri(4-pyridyl)-1,3,5-triazine (TPyTA) and 1,3-bis(trans-4-pyridylvinyl)benzene (BPyVB). X-ray crystallography study reveals that both polymers 1 and 2 crystallize in space group P2{sub 1}/c of the monoclinic system. The solid-state UV-vis absorption spectra show that 1 and 2 have maxium absorption onsets at 400 nm and 420 nm, respectively. TGA analysis indicates that 1 and 2 are stable up tomore » 110 Degree-Sign C and 210 Degree-Sign C. - Graphical abstract: Two novel one-dimensional coordination polymers, single helicate [Zn(SPh){sub 2}(TPyTA)(EG)]{sub n} (1) and zig-zag structure [Zn(SPh){sub 2}(BPyVB)]{sub n} (2), were synthesized. Solid-state UV-vis absorptions show that 1 and 2 have maxium absorption onsets at 400 nm and 420 nm, respectively. TGA analysis indicates that 1 and 2 are stable up to 110 Degree-Sign C and 210 Degree-Sign C. Highlights: Black-Right-Pointing-Pointer Two novel one-dimensional coordination polymers have been synthesized. Black-Right-Pointing-Pointer TPyTA results in helical structures in 1 while BPyVB leads to zig-zag chains in 2. Black-Right-Pointing-Pointer Solid-state UV-vis absorption spectra and TGA analysis of the title polymers were studied.« less

Hydrodynamics of bacterial colonies: Phase diagrams

NASA Astrophysics Data System (ADS)

Lega, J.; Passot, T.

2004-09-01

We present numerical simulations of a recent hydrodynamic model describing the growth of bacterial colonies on agar plates. We show that this model is able to qualitatively reproduce experimentally observed phase diagrams, which relate a colony shape to the initial quantity of nutrients on the plate and the initial wetness of the agar. We also discuss the principal features resulting from the interplay between hydrodynamic motions and colony growth, as described by our model.

Effects of thermal fluctuations and fluid compressibility on hydrodynamic synchronization of microrotors at finite oscillatory Reynolds number: a multiparticle collision dynamics simulation study.

PubMed

Theers, Mario; Winkler, Roland G

2014-08-28

We investigate the emergent dynamical behavior of hydrodynamically coupled microrotors by means of multiparticle collision dynamics (MPC) simulations. The two rotors are confined in a plane and move along circles driven by active forces. Comparing simulations to theoretical results based on linearized hydrodynamics, we demonstrate that time-dependent hydrodynamic interactions lead to synchronization of the rotational motion. Thermal noise implies large fluctuations of the phase-angle difference between the rotors, but synchronization prevails and the ensemble-averaged time dependence of the phase-angle difference agrees well with analytical predictions. Moreover, we demonstrate that compressibility effects lead to longer synchronization times. In addition, the relevance of the inertia terms of the Navier-Stokes equation are discussed, specifically the linear unsteady acceleration term characterized by the oscillatory Reynolds number ReT. We illustrate the continuous breakdown of synchronization with the Reynolds number ReT, in analogy to the continuous breakdown of the scallop theorem with decreasing Reynolds number.

Constraining the Properties of the Eta Carinae System via 3-D SPH Models of Space-Based Observations: The Absolute Orientation of the Binary Orbit

NASA Technical Reports Server (NTRS)

Madura, Thomas I.; Gull, Theodore R.; Owocki, Stanley P.; Okazaki, Atsuo T.; Russell, Christopher M. P.

2010-01-01

The extremely massive (> 90 Solar Mass) and luminous (= 5 x 10(exp 6) Solar Luminosity) star Eta Carinae, with its spectacular bipolar "Homunculus" nebula, comprises one of the most remarkable and intensely observed stellar systems in the galaxy. However, many of its underlying physical parameters remain a mystery. Multiwavelength variations observed to occur every 5.54 years are interpreted as being due to the collision of a massive wind from the primary star with the fast, less dense wind of a hot companion star in a highly elliptical (e approx. 0.9) orbit. Using three-dimensional (3-D) Smoothed Particle Hydrodynamics (SPH) simulations of the binary wind-wind collision in Eta Car, together with radiative transfer codes, we compute synthetic spectral images of [Fe III] emission line structures and compare them to existing Hubble Space Telescope/Space Telescope Imaging Spectrograph (HST/STIS) observations. We are thus able, for the first time, to constrain the absolute orientation of the binary orbit on the sky. An orbit with an inclination of i approx. 40deg, an argument of periapsis omega approx. 255deg, and a projected orbital axis with a position angle of approx. 312deg east of north provides the best fit to the observations, implying that the orbital axis is closely aligned in 3-1) space with the Homunculus symmetry axis, and that the companion star orbits clockwise on the sky relative to the primary.

Simulation of Shear and Bending Cracking in RC Beam: Material Model and its Application to Impact

NASA Astrophysics Data System (ADS)

Mokhatar, S. N.; Sonoda, Y.; Zuki, S. S. M.; Kamarudin, A. F.; Noh, M. S. Md

2018-04-01

This paper presents a simple and reliable non-linear numerical analysis incorporated with fully Lagrangian method namely Smoothed Particle Hydrodynamics (SPH) to predict the impact response of the reinforced concrete (RC) beam under impact loading. The analysis includes the simulation of the effects of high mass low-velocity impact load falling on beam structures. Three basic ideas to present the localized failure of structural elements are: (1) the accurate strength of concrete and steel reinforcement during the short period (dynamic), Dynamic Increase Factor (DIF) has been employed for the effect of strain rate on the compression and tensile strength (2) linear pressure-sensitive yield criteria (Drucker-Prager type) with a new volume dependent Plane-Cap (PC) hardening in the pre-peak regime is assumed for the concrete, meanwhile, shear-strain energy criterion (Von-Mises) is applied to steel reinforcement (3) two kinds of constitutive equation are introduced to simulate the crushing and bending cracking of the beam elements. Then, these numerical analysis results were compared with the experimental test results.

SphK1 inhibitor II (SKI-II) inhibits acute myelogenous leukemia cell growth in vitro and in vivo

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Li; Weng, Wei; Sun, Zhi-Xin

Previous studies have identified sphingosine kinase 1 (SphK1) as a potential drug target for treatment of acute myeloid leukemia (AML). In the current study, we investigated the potential anti-leukemic activity of a novel and specific SphK1 inhibitor, SKI-II. We demonstrated that SKI-II inhibited growth and survival of human AML cell lines (HL-60 and U937 cells). SKI-II was more efficient than two known SphK1 inhibitors SK1-I and FTY720 in inhibiting AML cells. Meanwhile, it induced dramatic apoptosis in above AML cells, and the cytotoxicity by SKI-II was almost reversed by the general caspase inhibitor z-VAD-fmk. SKI-II treatment inhibited SphK1 activation, andmore » concomitantly increased level of sphingosine-1-phosphate (S1P) precursor ceramide in AML cells. Conversely, exogenously-added S1P protected against SKI-II-induced cytotoxicity, while cell permeable short-chain ceramide (C6) aggravated SKI-II's lethality against AML cells. Notably, SKI-II induced potent apoptotic death in primary human AML cells, but was generally safe to the human peripheral blood mononuclear cells (PBMCs) isolated from healthy donors. In vivo, SKI-II administration suppressed growth of U937 leukemic xenograft tumors in severe combined immunodeficient (SCID) mice. These results suggest that SKI-II might be further investigated as a promising anti-AML agent. - Highlights: • SKI-II inhibits proliferation and survival of primary and transformed AML cells. • SKI-II induces apoptotic death of AML cells, but is safe to normal PBMCs. • SKI-II is more efficient than two known SphK1 inhibitors in inhibiting AML cells. • SKI-II inhibits SphK1 activity, while increasing ceramide production in AML cells. • SKI-II dose-dependently inhibits U937 xenograft growth in SCID mice.« less

Monte Carlo closure for moment-based transport schemes in general relativistic radiation hydrodynamic simulations

NASA Astrophysics Data System (ADS)

Foucart, Francois

2018-04-01

General relativistic radiation hydrodynamic simulations are necessary to accurately model a number of astrophysical systems involving black holes and neutron stars. Photon transport plays a crucial role in radiatively dominated accretion discs, while neutrino transport is critical to core-collapse supernovae and to the modelling of electromagnetic transients and nucleosynthesis in neutron star mergers. However, evolving the full Boltzmann equations of radiative transport is extremely expensive. Here, we describe the implementation in the general relativistic SPEC code of a cheaper radiation hydrodynamic method that theoretically converges to a solution of Boltzmann's equation in the limit of infinite numerical resources. The algorithm is based on a grey two-moment scheme, in which we evolve the energy density and momentum density of the radiation. Two-moment schemes require a closure that fills in missing information about the energy spectrum and higher order moments of the radiation. Instead of the approximate analytical closure currently used in core-collapse and merger simulations, we complement the two-moment scheme with a low-accuracy Monte Carlo evolution. The Monte Carlo results can provide any or all of the missing information in the evolution of the moments, as desired by the user. As a first test of our methods, we study a set of idealized problems demonstrating that our algorithm performs significantly better than existing analytical closures. We also discuss the current limitations of our method, in particular open questions regarding the stability of the fully coupled scheme.

Brownian dynamics simulations of lipid bilayer membrane with hydrodynamic interactions in LAMMPS

NASA Astrophysics Data System (ADS)

Fu, Szu-Pei; Young, Yuan-Nan; Peng, Zhangli; Yuan, Hongyan

2016-11-01

Lipid bilayer membranes have been extensively studied by coarse-grained molecular dynamics simulations. Numerical efficiencies have been reported in the cases of aggressive coarse-graining, where several lipids are coarse-grained into a particle of size 4 6 nm so that there is only one particle in the thickness direction. Yuan et al. proposed a pair-potential between these one-particle-thick coarse-grained lipid particles to capture the mechanical properties of a lipid bilayer membrane (such as gel-fluid-gas phase transitions of lipids, diffusion, and bending rigidity). In this work we implement such interaction potential in LAMMPS to simulate large-scale lipid systems such as vesicles and red blood cells (RBCs). We also consider the effect of cytoskeleton on the lipid membrane dynamics as a model for red blood cell (RBC) dynamics, and incorporate coarse-grained water molecules to account for hydrodynamic interactions. The interaction between the coarse-grained water molecules (explicit solvent molecules) is modeled as a Lennard-Jones (L-J) potential. We focus on two sets of LAMMPS simulations: 1. Vesicle shape transitions with varying enclosed volume; 2. RBC shape transitions with different enclosed volume. This work is funded by NSF under Grant DMS-1222550.

Brownian dynamics simulations of lipid bilayer membrane with hydrodynamic interactions in LAMMPS

NASA Astrophysics Data System (ADS)

Fu, Szu-Pei; Young, Yuan-Nan; Peng, Zhangli; Yuan, Hongyan

Lipid bilayer membranes have been extensively studied by coarse-grained molecular dynamics simulations. Numerical efficiency has been reported in the cases of aggressive coarse-graining, where several lipids are coarse-grained into a particle of size 4 6 nm so that there is only one particle in the thickness direction. Yuan et al. proposed a pair-potential between these one-particle-thick coarse-grained lipid particles to capture the mechanical properties of a lipid bilayer membrane (such as gel-fluid-gas phase transitions of lipids, diffusion, and bending rigidity). In this work we implement such interaction potential in LAMMPS to simulate large-scale lipid systems such as vesicles and red blood cells (RBCs). We also consider the effect of cytoskeleton on the lipid membrane dynamics as a model for red blood cell (RBC) dynamics, and incorporate coarse-grained water molecules to account for hydrodynamic interactions. The interaction between the coarse-grained water molecules (explicit solvent molecules) is modeled as a Lennard-Jones (L-J) potential. We focus on two sets of LAMMPS simulations: 1. Vesicle shape transitions with varying enclosed volume; 2. RBC shape transitions with different enclosed volume.

Identifying and analysing protostellar disc fragments in smoothed particle hydrodynamics simulations

NASA Astrophysics Data System (ADS)

Hall, Cassandra; Forgan, Duncan; Rice, Ken

2017-09-01

We present a new method of identifying protostellar disc fragments in a simulation based on density derivatives, and analyse our data using this and the existing CLUMPFIND method, which is based on an ordered search over all particles in gravitational potential energy. Using smoothed particle hydrodynamics, we carry out nine simulations of a 0.25 M⊙ disc around a 1 M⊙ star, all of which fragment to form at least two bound objects. We find that when using all particles ordered in gravitational potential space, only fragments that survive the duration of the simulation are detected. When we use the density derivative method, all fragments are detected, so the two methods are complementary, as using the two methods together allows us to identify all fragments, and to then determine those that are likely to be destroyed. We find a tentative empirical relationship between the dominant azimuthal wavenumber in the disc m and the maximum semimajor axis a fragment may achieve in a simulation, such that amax∝1/m. We find the fragment destruction rate to be around half that predicted from population synthesis models. This is due to fragment-fragment interactions in the early gas phase of the disc, which can cause scattering and eccentricity pumping on short time-scales, and affects the fragment's internal structure. We therefore caution that measurements of eccentricity as a function of semimajor axis may not necessarily constrain the formation mechanism of giant planets and brown dwarfs.

Hydrodynamic simulation and particle-tracking techniques for identification of source areas to public-water intakes on the St. Clair-Detroit river waterway in the Great Lakes Basin