Abstract:

The data includes .dat files in two directories: i. “flow field” and ii. “swimmers time history” (that can be plotted via Tecplot), containing the following information: The flow-field (i.e. u, v: the dimensionless horizontal and vertical components of fluid velocity as a function of space and time) generated by the motion of rod-shaped microswimmers in a viscoelastic fluid and time evolution of the position (i.e. x, y: the dimensionless horizontal and vertical coordinates of the rod’s center of mass) of each of the rod-shaped swimmers in the fluid domain. A ‘read-me’ file is included with the dataset that explains the definition of all variables present in the two directories.

Suggested Citation:

Gaojin Li, Arezoo Ardekani. 2017. Numerical investigation of collective motion of rod-shaped microorganisms in a viscoelastic fluid. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7K64G3D

Publications:

Li, G., & Ardekani, A. M. (2016). Collective Motion of Microorganisms in a Viscoelastic Fluid. Physical Review Letters, 117(11). doi:10.1103/physrevlett.117.118001

Purpose:

We study the effects of fluid viscoelasticity, characteristic of dispersant- or biofilm-coated interfaces, on the collective motion of rod-like micro-swimmers. We find that the fluid elasticity has a small effect on a suspension of pullers, for which the front half of the rod has a slip velocity and its latter half has a zero velocity, while it significantly affects the pushers, which is the opposite to the puller. The attraction and orientational ordering of the pushers are enhanced in viscoelastic fluids.

Data Parameters and Units:

Two types of swimmers are considered: pusher and puller. For a pusher swimmer, it has a slip velocity profile U=U_0*[tanh(10s/l)+1], where s=0 represents its head, and s=1 is its tail. A pusher has a zero velocity on the front half of its body and a slip velocity on the rear half of its body. A puller is the opposite of a pusher, with slip velocity on its front half and zero velocity on the rear half. The computational domain is a square of length L and is divided into 16 (or 32 for "De=0_puller_c=1" only) zones. In the "flow fields" directory, the fluid's velocity distribution in each of the zones is provided in a total of 16 .dat files (eg. plot0000000_000.dat to plot0000000_015.dat), one for each zone. For the case of "De=0_puller_c=1", the computational domain is divided into 32 files instead of 16. Collectively, these 16 (or 32 in case of "De=0_puller_c=1") files correspond to one time instant in the numerical simulation. The "swimmers time history" directory has files that store locations of all the rod-shaped swimmers (400 in total) and other pertinent parameters like swimming orientations and velocities. All the results are reported as dimensionless numbers that have been normalized as follows: the length is scaled by swimmer length l, velocity by U0/2 (which is the characteristic velocity of an 'isolated' micro-swimmer), time by 2l/U0, and pressure and stress by rho*mu*U0/2l, where rho and mu are the fluid density and viscosity, respectively. The 17th file i.e. 'plot0000000_016.dat' (or 33rd i.e. 'plot0000000_032.dat', in case of "De=0_puller_c=1") contains the positions and orientational angles for the swimmers at each time instant of the numerical simulation.

Methods:

Fully resolved numerical solutions to the Navier-Stokes equations coupled with an Oldroyd-B constitutive equation are obtained. The numerical method employed is a finite volume method and distributed Lagrangian multiplier method, for more details see [1, 2]. 5. References: [1] Ardekani, A.M., Dabiri, S. and Rangel, R.H., 2008. “Collision of multi-particle and general shape objects in a viscous fluid”, Journal of Computational Physics, 227 (24), p.10094; [2] Li, G. and Ardekani, A.M., 2015. “Undulatory swimming in non-Newtonian fluids”, Journal of Fluid Mechanics, 784, p.R4.

Individual Files: