Skip to main content
Article thumbnail
Location of Repository

An efficient multi-scale modelling approach for ssDNA motion in fluid flow

By Matyas Benke, Evgeniy Shapiro and Dimitris Drikakis


The paper presents a multi-scale modelling approach for simulating macromolecules in fluid flows. Macromolecule transport at low number densities is frequently encountered in biomedical devices, such as separators, detection and analysis systems. Accurate modelling of this process is challenging due to the wide range of physical scales involved. The continuum approach is not valid for low solute concentrations, but the large timescales of the fluid flow make purely molecular simulations prohibitively expensive. A promising multi-scale modelling strategy is provided by the meta-modelling approach considered in this paper. Meta-models are based on the coupled solution of fluid flow equations and equations of motion for a simplified mechanical model of macromolecules. The approach enables simulation of individual macromolecules at macroscopic time scales. Meta-models often rely on particle-corrector algorithms, which impose length constraints on the mechanical model. Lack of robustness of the particle- corrector algorithm employed can lead to slow convergence and numerical instability. A new FAst Linear COrrector (FALCO) algorithm is introduced in this paper, which significantly improves computational efficiency in comparison with the widely used SHAKE algorithm. Validation of the new particle corrector against a simple analytic solution is performed and improved convergence is demonstrated for ssDNA motion in a lid-driven micro-cavity

Topics: Multi-scale modelling, DNA, Macromolecule transport, Meta-modelling, Particle corrector.
Publisher: Elsevier Science B.V., Amsterdam
Year: 2008
DOI identifier: 10.1016/S1672-6529(08)60174-2
OAI identifier:
Provided by: Cranfield CERES

Suggested articles


  1. (2005). A tightly coupled particle-fluid model for DNA-laden flows in complex microscale geometries.
  2. (2000). A transmission imaging spectrograph and microfabricated channel system for DNA analysis. Electrophoresis, doi
  3. Addendum to “Monomer motion in single- and double-stranded DNA coils”. arXiv:cond-mat/0701523v1 [cond-mat.soft],
  4. (2002). Chaotic mixer for microchannels. Science,
  5. (1959). Classical mechanics. doi
  6. (2005). Computational Model with Experimental Validation for DNA Flow in Microchannels. NSTI-Nanotechnology,
  7. (2008). Coupling strategies for hybrid molecular-continuum22 simulation methods, doi
  8. (2003). Deformation of DNA molecules by hydrodynamic focusing. doi
  9. (2002). Design and fabrication of a hydrodynamic chromatography chip. Sensors and Actuators doi
  10. (2002). Detection of homocysteine by conventional and microchip capillary electrophoresis/electrochemistry. Electrophoresis, doi
  11. (1997). Diffusion: Mass Transfer in Fluid Systems. doi
  12. (2004). Engineering flows in small devices: Microfluidics toward a lab-on-a-chip. Annual Review of Fluid Mechanics, doi
  13. (2002). High-resolution chiral separation using microfluidics-based membrane chromatography. doi
  14. (2004). High-Resolution Methods for Incompressible and Low-Speed Flows. doi
  15. (2004). Introduction: mixing in microfluidics. doi
  16. (2005). Liquids: The holy grail of microfluidic modelling. doi
  17. (1983). Low Reynolds number hydrodynamics. Hague : Martinus Nijhoff Publishers, doi
  18. (2005). Microflows and Nanoflows: Fundamentals and Simulation. doi
  19. (2006). Microfluidic Cell Optimization for Polymer Membrane Fabrication. doi
  20. (2006). Microfluidic systems for in situ formation of nylon 6,6 membranes, doi
  21. (2005). Microfluidics: Fluid physics at the nanoliter scale. Reviews of Modern Physics, doi
  22. (2005). Micromixers - a review. doi
  23. (1999). Microscale technology. Chemical and Engineering News, doi
  24. (1994). Migration of macromolecules under flow: the physical origin and engineering implications. Chemical Engineering Science, doi
  25. (2006). Non-Conservative and Conservative Formulations of Characteristics-Based Numerical Reconstructions for Incompressible Flows. doi
  26. (1977). Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. doi
  27. (1968). Numerical Solution of the Navier-Stokes Equations. doi
  28. (1996). Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science, doi
  29. (2005). Part Separation doi
  30. (2006). Pressure-driven transport of confined DNA polymers in fluididc channels. PNAS, doi
  31. (1999). Radial Capillary Array Electrophoresis Microplate and Scanner for High-Performance Nucleic Acid Analysis. Analytical Chemistry, doi
  32. (2000). Single-molecule studies of DNA mechanics. Current opinion in structural biology, doi
  33. (2002). The analysis of uric acid in urine using microchip capillary electrophoresis with electrochemical detection. Electrophoresis, doi
  34. (2004). The effect of velocity and extensional strain rate on enhancing DNA hybridization. doi
  35. (2006). The origins and the future of microfluidics. Nature, doi
  36. (1986). The theory of polymer dynamics. doi

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.