An efficient particle tracking algorithm for large-scale parallel pseudo-spectral simulations of turbulence

Lalescu, Cristian; Bramas, Bérenger; Rampp, Markus; Wilczek, Michael

doi:10.1016/j.cpc.2022.108406

Cited by 6 publications

(8 citation statements)

References 60 publications

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“…Data Availability. The code for the turbulence simulations data has been deposited in a publicly accessible repository (https://gitlab.mpcdf.mpg.de/TurTLE/ turtle) and is described in (50). The relevant study data is displayed in the manuscript and the SI Appendix.…”

Section: Methodsmentioning

confidence: 99%

Elongation enhances encounter rates between phytoplankton in turbulence

Arguedas-Leiva

Słomka

Lalescu

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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Phytoplankton come in a stunning variety of shapes but elongated morphologies dominate—typically 50% of species have aspect ratio above 5, and bloom-forming species often form chains whose aspect ratios can exceed 100. How elongation affects encounter rates between phytoplankton in turbulence has remained unknown, yet encounters control the formation of marine snow in the ocean. Here, we present simulations of encounters among elongated phytoplankton in turbulence, showing that encounter rates between neutrally buoyant elongated cells are up to 10-fold higher than for spherical cells and even higher when cells sink. Consequently, we predict that elongation can significantly speed up the formation of marine snow compared to spherical cells. This unexpectedly large effect of morphology in driving encounter rates among plankton provides a potential mechanistic explanation for the rapid clearance of many phytoplankton blooms.

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Section: Methodsmentioning

confidence: 99%

Elongation enhances encounter rates between phytoplankton in turbulence

Arguedas-Leiva

Słomka

Lalescu

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

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“…In our code we solve this equation, and then obtain the velocity field by means of Biot-Savart law and inverse Fourier transform. We use our in-house code TurTLE [61] to integrate the vorticity fomulation (2.60). We use a third order Runge-Kutta method for time integration and use the FFTW library [62] to perform the Fourier transform.…”

Section: Pseudo-spectral Approach To Solving the Navier-stokes Equationsmentioning

confidence: 99%

“…The code TurTLE [61] implements particle position and orientation via time integration of the equations of motion. This is done with a second order Adams-Bashforth time integrating scheme.…”

Section: Particle Integrationmentioning

confidence: 99%

“…The particles can be coupled to the value of the velocity, vorticity, or gradient fields at each particle position. This is done via an efficient and scalable interpolation scheme [61]. The coupling is one way, as the particles can be coupled to the fluid flow, but they themselves have no effect on the undelying flow.…”

Section: Particle Integrationmentioning

confidence: 99%

“…We perform fully resolved direct numerical simulations of the incompressible Navier-Stokes equations in the vorticity formulation with our code TurTLE. This fluid flow solver is a highly parallelized pseudo-spectral code that allows for the integration of particle species advected with the fluid flow [61]. The incompressible Navier-Stokes equations take the form…”

Section: Turbulence Simulationsmentioning

confidence: 99%

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Physical modeling of motile and sedimenting plankton: from simple flows to turbulence

Leiva¹

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Planktonic microorganisms play a fundamental role in oceanic ecology and chemical cycles. Different planktonic species are found at various levels of the oceanic trophic chain, ranging from photosynthetic organisms to grazing species higher in the food chain. Many planktonic species have developed migration strategies to aid their survival. This includes motility and density regulation. Physical aspects, such as transport and collision rates, have a direct impact on planktonic survival and are influenced by the planktonic migration strategies. Furthermore, collision rates between planktonic organisms also play an important role in the formation of macroscopic plankton blooms. These have a direct effect on the ecology of oceans and lakes. In this dissertation we use physical modeling to study motile and sedimenting microorganisms in a fluid flow. We aim at shedding light on the key features of microorganism dynamics in fluid flows as a function of their key parameters: shape, motility, and density offset.In chapter 1 we introduce the biological setting of plankton, and give a very brief overview of the physical modeling approaches for plankton in fluid flows. Subsequently in chapter 2 we introduce the theoretical framework of turbulence and the methodology of our numerical simulations.In chapter 3 we start by examining microswimmers in a simple two-dimensional toy-model. We use methods from dynamical systems theory to uncover the role played by shape and motility in determining the microorganism dynamics in this simple setting. We explicitly identify the Hamiltonian dynamics followed by spherical microswimmers. Additionally, we find that elongated microswimmers more easily escape simple vortex structures than other shapes. In chapter 4 we then move on to ellipsoidal microswimmers in realistic mild turbulent flows. We analyze transport and rotation rates of motile ellipsoids. We find that elongated microswimmers have an advantage in transport, which is in part due to shape-dependent rotation rates. We also investigated the collision rates of motile spheres, and we were able to extract a master curve interpolating between the passive and motile limits for different sized spheres. We quantified the effect of motility and found that even very small motility greatly enhances collision rates.In chapter 5 we study of sedimentation of elongated microorganisms in mild turbulence. We measure the collision rates of elongated microorganisms in terms of size, energy dissipation rate, and aspect ratio. We then find a master curve interpolating between a passive particle and a sedimentation dominated limit. We characterize the role played by shape, which increases collision rates of elongated microorganisms in comparison with equal-volume spheres. This shape-induced enhancement helps to explain the timescales for formation of blooms of elongated planktonic species. In summary, in this dissertation we study the effect of shape, motility, and density regulation on physical models of planktonic microorganisms. Our findings help to ...

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The statistical geometry of material loops in turbulence

et al. 2022

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Material elements – which are lines, surfaces, or volumes behaving as passive, non-diffusive markers – provide an inherently geometric window into the intricate dynamics of chaotic flows. Their stretching and folding dynamics has immediate implications for mixing in the oceans or the atmosphere, as well as the emergence of self-sustained dynamos in astrophysical settings. Here, we uncover robust statistical properties of an ensemble of material loops in a turbulent environment. Our approach combines high-resolution direct numerical simulations of Navier-Stokes turbulence, stochastic models, and dynamical systems techniques to reveal predictable, universal features of these complex objects. We show that the loop curvature statistics become stationary through a dynamical formation process of high-curvature folds, leading to distributions with power-law tails whose exponents are determined by the large-deviations statistics of finite-time Lyapunov exponents of the flow. This prediction applies to advected material lines in a broad range of chaotic flows. To complement this dynamical picture, we confirm our theory in the analytically tractable Kraichnan model with an exact Fokker-Planck approach.

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An efficient particle tracking algorithm for large-scale parallel pseudo-spectral simulations of turbulence

Cited by 6 publications

References 60 publications

Elongation enhances encounter rates between phytoplankton in turbulence

Elongation enhances encounter rates between phytoplankton in turbulence

Physical modeling of motile and sedimenting plankton: from simple flows to turbulence

The statistical geometry of material loops in turbulence

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