scholarly journals Adaptive preferential sampling in phylodynamics with an application to SARS-CoV-2

Author(s):  
Lorenzo Cappello ◽  
Julia A. Palacios
2016 ◽  
Vol 798 ◽  
pp. 187-200 ◽  
Author(s):  
S. Vajedi ◽  
K. Gustavsson ◽  
B. Mehlig ◽  
L. Biferale

The distribution of particle accelerations in turbulence is intermittent, with non-Gaussian tails that are quite different for light and heavy particles. In this article we analyse a closure scheme for the acceleration fluctuations of light and heavy inertial particles in turbulence, formulated in terms of Lagrangian correlation functions of fluid tracers. We compute the variance and the flatness of inertial-particle accelerations and we discuss their dependency on the Stokes number. The closure incorporates effects induced by the Lagrangian correlations along the trajectories of fluid tracers, and its predictions agree well with results of direct numerical simulations of inertial particles in turbulence, provided that the effects induced by inertial preferential sampling of heavy/light particles outside/inside vortices are negligible. In particular, the scheme predicts the correct functional behaviour of the acceleration variance, as a function of $St$, as well as the presence of a minimum/maximum for the flatness of the acceleration of heavy/light particles, in good qualitative agreement with numerical data. We also show that the closure works well when applied to the Lagrangian evolution of particles using a stochastic surrogate for the underlying Eulerian velocity field. Our results support the conclusion that there exist important contributions to the statistics of the acceleration of inertial particles independent of the preferential sampling. For heavy particles we observe deviations between the predictions of the closure scheme and direct numerical simulations, at Stokes numbers of order unity. For light particles the deviation occurs for larger Stokes numbers.


2011 ◽  
Vol 22 (2) ◽  
pp. 281-291 ◽  
Author(s):  
Dana Michalcová ◽  
Samuel Lvončík ◽  
Milan Chytrý ◽  
Ondřej Hájek

2018 ◽  
Vol 121 (24) ◽  
Author(s):  
Jason R. Picardo ◽  
Dario Vincenzi ◽  
Nairita Pal ◽  
Samriddhi Sankar Ray

2012 ◽  
pp. 223-226
Author(s):  
D Clifford ◽  
P Kuhnert ◽  
M Dobbie ◽  
J Baldock ◽  
B Harch ◽  
...  

2018 ◽  
Vol 68 (1) ◽  
pp. 181-198 ◽  
Author(s):  
Daniel Dinsdale ◽  
Matias Salibian‐Barrera

2018 ◽  
Vol 856 ◽  
Author(s):  
M. Borgnino ◽  
G. Boffetta ◽  
F. De Lillo ◽  
M. Cencini

We study the dynamics and the statistics of dilute suspensions of gyrotactic swimmers, a model for many aquatic motile microorganisms. By means of extensive numerical simulations of the Navier–Stokes equations at different Reynolds numbers, we investigate preferential sampling and small-scale clustering as a function of the swimming (stability and speed) and shape parameters, considering in particular the limits of spherical and rod-like particles. While spherical swimmers preferentially sample local downwelling flow, for elongated swimmers we observe a transition from downwelling to upwelling regions at sufficiently high swimming speed. The spatial distribution of both spherical and elongated swimmers is found to be fractal at small scales in a wide range of swimming parameters. The direct comparison between the different shapes shows that spherical swimmers are more clusterized at small stability and speed numbers, while for large values of the parameters elongated cells concentrate more. The relevance of our results for phytoplankton swimming in the ocean is briefly discussed.


Author(s):  
Peter J. Diggle ◽  
Raquel Menezes ◽  
Ting-li Su

2019 ◽  
Vol 877 ◽  
pp. 82-104 ◽  
Author(s):  
M. Houssem Kasbaoui ◽  
Donald L. Koch ◽  
Olivier Desjardins

In this study, we address the modification of sheared turbulence by dispersed inertial particles. The preferential sampling of the straining regions of the flow by inertial particles in turbulence leads to an inhomogeneous distribution of particles. The strong gravitational loading exerted by the highly concentrated regions results in anisotropic alteration of turbulence at small scales in the direction of gravity. These effects are investigated in a rapid distortion theory (RDT) extended for two-way coupled particle-laden flows. To make the analysis tractable, we assume that particles have small but non-zero inertia. In the classical results for single-phase flows, the RDT assumption of fast shearing compared to the turbulence time scales leads to the distortion and shear-induced production of turbulence. In particle-laden turbulence, the coupling between the two phases under rapid shearing induces number density fluctuations that convert gravitational potential energy to turbulent kinetic energy and modulate the turbulence spectrum in a manner that increases with mass loading. Turbulence statistics obtained from RDT are compared with Euler–Lagrange simulations of homogeneously sheared particle-laden turbulence.


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