scholarly journals The influence of motility on bacterial accumulation in a microporous channel

Soft Matter ◽  
2021 ◽  
Author(s):  
Miru Lee ◽  
Christoph Lohrmann ◽  
Kai Szuttor ◽  
Harold Auradou ◽  
Christian Holm
Keyword(s):  
Molecular Dynamics ◽  
Porous Media ◽  
Molecular Dynamics Simulations ◽  
Lattice Boltzmann ◽  
Square Channel ◽  
Cylindrical Obstacle ◽  
Bacterial Accumulation ◽  
Dynamics Simulations ◽  
Transport Of Bacteria

We study the transport of bacteria in a porous media modeled by a square channel containing one cylindrical obstacle via molecular dynamics simulations coupled to a lattice Boltzmann fluid.

Molecular Dynamics Simulations of Benchmark Geometries Representing a Flow Through Porous Media

2014 ◽  
Author(s):  
Marc-Florian Uth ◽  
Henrik Asmuth ◽  
Christian Windt ◽  
Heinz Herwig
Keyword(s):  
Molecular Dynamics ◽  
Porous Media ◽  
Fluid Flow ◽  
Molecular Dynamics Simulations ◽  
Complex Geometries ◽  
Pore Scale ◽  
Flow Through Porous Media ◽  
Flow Through ◽  
Dynamics Simulations ◽  
The Continuum

Fluid Dynamics Simulations are often based on continuum assumptions that, for micro- or nano-flows, are extended by models that take into account special phenomena (e. g. wall slip) that occour in these dimensions. On the nano-scale not only the near wall layers show peculiarities. Especially for liquids the bulk flow deviates from smooth profiles and thus strongly differs from continuum theory. So far mainly the flow in straight channels has been investigated with Molecular Dynamics Simulations. In real porous media such perfectly flat channels do not appear. Thus, to analyze the applicability of the continuum assumption for the simulation of fluid flow on the pore-scale the type of geometries that are evaluated has to be extended. Therefore in this paper we present the results of Molecular Dynamics Simulations of a liquid in a Couette flow, the flow through a straight channel, a bend and through an array of cylinders. We present the results for varying wall-fluid potentials, shear rates, and temperatures and compare the results to the validated data from a finite volume solution of the Navier-Stokes-Equations for the same geometries. As a result we show the difficulties due to complex geometries for the simulation with Molecular Dynamics. Also the boundary conditions for Molecular Dynamics Simulations, like the thermostat or the wall model are discussed. We show that for some parameter sets, a critical behaviour can be observed for the more complex geometries. Such results are evaluated to show the differences between MD and FVM simulations. It turns out however, that the limits of the continuum assumptions are very different for different geometries. In complex geometries the minimum characteristic size can be much smaller than in straight channels. Hence the scope of continuum methods for the simulation of fluid flow through porous media on the pore scale is larger than expected.

Polymer margination in uniform shear flows

Soft Matter ◽  
2018 ◽  
Vol 14 (45) ◽  
pp. 9209-9219 ◽  
Author(s):  
Venkat Balasubramanian ◽  
Colin Denniston
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lattice Boltzmann ◽  
Shear Flows ◽  
Uniform Shear ◽  
Dynamics Simulations

We address the issue of polymer margination (migration towards surfaces) in uniform shear flows through extensive LBMD (lattice-Boltzmann molecular dynamics) simulations.

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