Numerical Simulation of Particle Transport in a Drift Ratchet

The directed transport of microparticles depending on their size is the basis for particle sorting methods that are of utmost importance in, for example, life sciences. A drift ratchet is a Brownian motor that allows for such a directed transport. Hereby, the particle motion is induced by a combination of the Brownian motion and asymmetries stemming, for example, from the domain's geometry, electrical fields, or transient pressure boundary conditions. We simulate a particular drift ratchet which consists of a matrix of pores with asymmetrically oscillating diameter wherein a fluid with suspended particles is pumped forward and backward, and where the particles' long-term transport direction depends on their size. Thus, this setup allows for continuous and parallel particle separation, which has been shown experimentally. However, for a deeper understanding and for an optimized parameters' choice, further investigations, i.e., simulations, are necessary. In this paper, we present first results achieved with our parallel three-dimensional simulation codes applied to a still simplified scenario. This simplification is necessary to isolate different phenomena (e.g., asymmetries and Brownian motion) to check their relevance for the particle transport. The simulation codes are based on (adaptive) Cartesian grids in combination with finite volume and finite element discretizations. Cartesian grids allow for a very efficient implementation of the solver algorithms and an efficient balanced parallelization via domain decomposition. The achieved simulation results show the effectiveness of our approach and give some strong hints on a directed particle transport already with the simplified model we used here.

[1]  Katherine A. Yelick,et al.  Distributed Immersed Boundary Simulation in Titanium , 2006, SIAM J. Sci. Comput..

[2]  Hans-Joachim Bungartz,et al.  CARTESIAN DISCRETISATIONS FOR FLUID-STRUCTURE INTERACTION { CONSISTENT FORCES , 2006 .

[3]  M. F. Tomé,et al.  GENSMAC: a computational marker and cell method for free surface flows in general domains , 1994 .

[4]  Maximilian Emans Numerische Simulation des unterkühlten Blasensiedens in turbulenter Strömung , 2003 .

[5]  F. Harlow,et al.  Numerical Calculation of Time‐Dependent Viscous Incompressible Flow of Fluid with Free Surface , 1965 .

[6]  C. Farhat,et al.  Partitioned procedures for the transient solution of coupled aroelastic problems Part I: Model problem, theory and two-dimensional application , 1995 .

[7]  William F. Mitchell,et al.  A refinement-tree based partitioning method for dynamic load balancing with adaptively refined grids , 2007, J. Parallel Distributed Comput..

[8]  C. Zenger,et al.  An efficient method for the prediction of the motion of individual bubbles , 2005 .

[9]  Thomas F. Miller,et al.  Symplectic quaternion scheme for biophysical molecular dynamics , 2002 .

[10]  J. Szmelter Incompressible flow and the finite element method , 2001 .

[11]  P. Reimann Brownian motors: noisy transport far from equilibrium , 2000, cond-mat/0010237.

[12]  A. Castellazzi,et al.  Electrothermal simulation of multichip-modules with novel transient thermal model and time-dependent boundary conditions , 2006, IEEE Transactions on Power Electronics.

[13]  Sven Matthias,et al.  Asymmetric pores in a silicon membrane acting as massively parallel brownian ratchets , 2003, Nature.

[14]  Ramses van Zon,et al.  Numerical implementation of the exact dynamics of free rigid bodies , 2006, J. Comput. Phys..

[15]  R. Rannacher,et al.  Benchmark Computations of Laminar Flow Around a Cylinder , 1996 .

[16]  M. Schindler Free-Surface Microflows and Particle Transport , 2006 .

[17]  Ulrich Rüde,et al.  Cache Optimization for Structured and Unstructured Grid Multigrid , 2000 .

[18]  Peter Hänggi,et al.  Membranes for Micropumps from Macroporous Silicon , 2000 .

[19]  Miriam Mehl,et al.  A cache‐oblivious self‐adaptive full multigrid method , 2006, Numer. Linear Algebra Appl..

[20]  Arthur Veldman,et al.  Symmetry-Preserving Discretization of Turbulent Channel Flow , 2002 .

[21]  G A Griess,et al.  Advances in the separation of bacteriophages and related particles. , 1999, Journal of chromatography. B, Biomedical sciences and applications.

[22]  Suncica Canic,et al.  Effective Equations Modeling the Flow of a Viscous Incompressible Fluid through a Long Elastic Tube Arising in the Study of Blood Flow through Small Arteries , 2003, SIAM J. Appl. Dyn. Syst..

[23]  F. Marchesoni,et al.  Brownian motors , 2004, cond-mat/0410033.

[24]  Michael Bader,et al.  An Octree-Based Approach for Fast Elliptic Solvers , 2002 .

[25]  Charbel Farhat,et al.  Partitioned procedures for the transient solution of coupled aeroelastic problems , 2001 .

[26]  Miriam Mehl,et al.  A Cache-Aware Algorithm for PDEs on Hierarchical Data Structures Based on Space-Filling Curves , 2006, SIAM J. Sci. Comput..

[27]  A. Chorin Numerical Solution of the Navier-Stokes Equations* , 1989 .

[28]  Hans-Joachim Bungartz,et al.  Fluid-Structure Interaction on Cartesian Grids: Flow Simulation and Coupling Environment , 2006 .

[29]  Ulrich Rüde,et al.  Memory Characteristics of Iterative Methods , 1999, SC.

[30]  Peter Hänggi,et al.  Introduction to the physics of Brownian motors , 2001 .

[31]  Haibo Dong,et al.  Towards Numerical Simulation of Flapping Foils on Fixed Cartesian Grids , 2005 .

[32]  David Rickwood,et al.  Gel electrophoresis of nucleic acids : a practical approach , 1982 .

[33]  Ralf-Peter Mundani Hierarchische Geometriemodelle zur Einbettung verteilter Simulationsaufgaben , 2006 .

[34]  Philippe Destuynder,et al.  A Noise Control Problem Arising in a Flow Duct , 2004, SIAM J. Appl. Math..

[35]  Hans-Joachim Bungartz,et al.  A Parallel Adaptive Cartesian PDE Solver Using Space-Filling Curves , 2006, Euro-Par.

[36]  Weigang Wang,et al.  Special Bilinear Quadrilateral Elements For Locally Refined Finite Element Grids , 2000, SIAM J. Sci. Comput..

[37]  Reimann,et al.  Drift ratchet , 2000, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[38]  Ruo Li,et al.  Moving Mesh Finite Element Methods for the Incompressible Navier-Stokes Equations , 2005, SIAM J. Sci. Comput..