Modeling and high performance simulation of electrophoretic techniques in microfluidic chips

Microfluidics and Nanofluidics

Volumn 10, Issue 1, 2011, Pages 187-198

  Kler, Pablo A ^a   Berli, Claudio L A ^a,b   Guarnieri, Fabio A ^a,c  

^a Centro Regional de Investigacion y Desarrollo de Santa Fe   (Argentina)

^b Ciudad Universitaria   (Argentina)

^c UNIVERSIDAD NACIONAL DE ENTRE RÍOS   (Argentina)

Author keywords

Electrophoresis; Microfluidic chips; Numerical model; PETSc FEM

Indexed keywords

3-D MICROFLUIDIC; ANALYTICAL TECHNIQUES; CAPILLARY ZONE ELECTROPHORESIS; CHANNEL WALL; COMMERCIAL SOFTWARE; ELECTRICAL PHENOMENA; ELECTROPHORETIC SEPARATIONS; FREE-FLOW ELECTROPHORESIS; HIGH PERFORMANCE PARALLEL COMPUTING; HIGH-PERFORMANCE SIMULATION; ISOELECTRIC FOCUSING; ISOTACHOPHORESIS; LAB-ON-A-CHIP TECHNOLOGY; MASS TRANSPORT; MICRO-FLUIDIC DEVICES; MICROFLUIDIC CHIP; MICROFLUIDIC CHIPS; MULTI-PHYSICS; NUMERICAL CALCULATION; NUMERICAL EFFICIENCY; NUMERICAL MODELS; PETSC-FEM; PRECONDITIONERS; PROTOTYPING; TIME-DEPENDENT; TWO DIMENSIONAL ELECTROPHORESIS;

CAPILLARY ELECTROPHORESIS; ELECTROCHEMISTRY; FLUIDIC DEVICES; IONIC STRENGTH; MICROFLUIDICS; NUMERICAL METHODS; PARALLEL ARCHITECTURES; THREE DIMENSIONAL;

MATHEMATICAL MODELS;

EID: 79551501323     PISSN: 16134982     EISSN: 16134990     Source Type: Journal    
DOI: 10.1007/s10404-010-0660-x     Document Type: Article

References (55)

1. JW Albrecht J El-Ali KF Jensen 2007 Cascaded free-flow isoelectric focusing for improved focusing speed and resolution Anal Chem 79 9364 9371 10.1021/ac071574q
2. I Arnaud J Josserand J Rossier H Girault 2002 Finite element simulation of off-gel buffering Electrophoresis 23 3253 3261 10.1002/1522-2683(200210)23: 19<3253::AID-ELPS3253>3.0.CO;2-4
3. Balay S, Buschelman K, Gropp WD, Kaushik D, Knepley MG, McInnes LC, Smith BF, Zhang H (2008) PETSc Web page. http://www.mcs.anl.gov/petsc
4. DP Barz 2009 Comprehensive model of electrokinetic flow and migration in microchannels with conductivity gradients Microfluid Nanofluid 7 2 249 265 10.1007/s10404-008-0382-5
5. M Bercovici SK Lele JG Santiago 2009 Open source simulation tool for electrophoretic stacking, focusing, and separation J Chromatogr A 1216 1008 1018 10.1016/j.chroma.2008.12.022
6. CLA Berli 2008 Equivalent circuit modeling of electrokinetically driven analytical microsystems Microfluid Nanofluid 4 5 391 399 10.1007/s10404-007- 0191-2
7. CLA Berli M Piaggio J Deiber 2003 Modeling the zeta potential of silica capillaries in relation to the background electrolyte composition Electrophoresis 24 1587 1595 10.1002/elps.200305371
8. F Bianchi R Ferrigno H Girault 2000 Finite element simulation of an electroosmotic-driven flow division at a T-junction of microscale dimensions Anal Chem 72 9 1987 1993 10.1021/ac991225z
9. E Brunet A Adjari 2004 Generalized Onsager relations for electrokinetic effects in anisotropic and heterogeneous geometries Phys Rev E. 69 1 016,306 10.1103/PhysRevE.69.016306
10. XC Cai DE Keyes 2002 Nonlinearly preconditioned inexact newton algorithms SIAM J Sci Comput 24 1 183 200 1015.65058 10.1137/S106482750037620X 1924420
11. A Chatterjee 2003 Generalized numerical formulations for multi-physics microfluidics-type applications J Micromech Microeng 13 758 767 10.1088/0960-1317/13/5/331
12. M Chau P Spiteri R Guivarich H Boisson 2008 Parallel asynchronous iterations for the solution of a 3d continuous flow electrophoresis problem Comput Fluid 37 9 1126 1137 10.1016/j.compfluid.2007.06.006
13. Craven TJ, Rees JM, Zimmerman WB (2008) On slip velocity boundary conditions for electroosmotic flow near sharp corners. Phys Fluids 20(4):043,603
14. L Dalcín R Paz MSJ D'Elia 2008 MPI for Python: performance improvements and MPI-2 extensions J Parallel Distr Comput 68 5 655 662 10.1016/j.jpdc.2007.09.005
15. D Erickson 2005 Towards numerical prototyping of labs-on-chip: modeling for integrated microfluidic devices Microfluid Nanofluid 1 4 301 318 10.1007/s10404-005-0041-z
16. S Ermakov S Jacobson J Ramsey 1998 Computer simulations of electrokinetic transport in microfabricated channel structures Anal Chem 70 21 4494 4504 10.1021/ac980551w
17. S Ermakov S Jacobson J Ramsey 2000 Computer simulations of electrokinetic injection techniques in microfluidic devices Anal Chem 72 15 3512 3517 10.1021/ac991474n
18. A Herr J Molho J Santiago M Mungal T Kenny M Garguilo 2000 Electroosmotic capillary flow with nonuniform zeta potential Anal Chem 72 1053 1057 10.1021/ac990489i
19. A Herr J Molho K Drouvalakis J Mikkelsen P Utz J Santiago T Kenny 2003 On-chip coupling of isoelectric focusing and free solution electrophoresis for multidimensional separations Anal Chem 75 1180 1187 10.1021/ac026239a
20. V Hruska M Jaros B Gas 2006 Simul 5-free dynamic simulator of electrophoresis Electrophoresis 27 984 991 10.1002/elps.200500756
21. Hunter R (2001) Foundations of colloid science, 2nd edn. Oxford University Press, Oxford
22. BJ Kirby EF Hasselbrink Jr 2004 Zeta potential of microfluidic substrates: 1. theory, experimental techniques, and effects on separations Electrophoresis 25 187 202 10.1002/elps.200305754
23. PA Kler EJ López LD Dalcín FA Guarnieri MA Storti 2009 High performance simulations of electrokinetic flow and transport in microfluidic chips Comput Method Appl M 198 30-32 2360 2367 10.1016/j.cma.2009.02.028
24. D Kohlheyer GAJ Besselink S Schlautmann RBM Schasfoort 2006 Free-flow zone electrophoresis and isoelectric focusing using a microfabricated glass device with ion permeable membranes Lab Chip 6 374 380 10.1039/b514731j
25. D Kohlheyer JCT Eijkel A van den Berg RBM Schasfoort 2008 Miniaturizing free-flow electrophoresis a critical review Electrophoresis 29 5 977 993 10.1002/elps.200700725
26. Landers JP (2007) Handbook of capillary and microchip electrophoresis and associated microtechniques, 3rd edn. CRC Press, Boca Raton
27. Li D (2004) Electrokinetics in microfluidics. Elsevier Academic Press, Amsterdam
28. JM MacInnes 2002 Computation of reacting electrokinetic flow in microchannel geometries Chem Eng Sci 57 21 4539 4558 10.1016/S0009-2509(02) 00311-1
29. J MacInnes X Du R Allen 2003 Prediction of electrokinetic and pressure flow in a microchannel T-junction Phys Fluids 15 7 1992 2005 10.1063/1.1580479
30. A Manz N Graber H Widmer 1990 Miniaturized total chemical analysis systems: a novel concept for chemical sensing Sens Actuators B 1 244 248 10.1016/0925-4005(90)80209-I
31. O Palusinski A Graham R Mosher M Bier D Saville 1986 Theory of electrophoretic separations. part ii: construction of a numerical scheme and its applications AICHE J 32 2 215 223 10.1002/aic.690320207
32. N Patankar H Hu 1998 Numerical simulation of electroosmotic flow Anal Chem 70 9 1870 1881 10.1021/ac970846u
33. Y Peng A Pallandre NT Tran M Taverna 2008 Recent innovations in protein separation on microchips by electrophoretic methods Electrophoresis 29 1 157 178 10.1002/elps.200700347
34. JD Posner JG Santiago 2006 Convective instability of electrokinetic flows in a cross-shaped microchannel J Fluid Mech 555 1 1 42 1156.76331 10.1017/S0022112005008542
35. Probstein R (2003) Physicochemical hydrodynamics. An introduction, 2nd edn. Wiley-Interscience, New York
36. D Reyes D Iossifidis P Auroux A Manz 2002 Micro total analysis systems. 1. introduction, theory, and technology Anal Chem 74 12 2623 2636 10.1021/ac0202435
37. Sandia NL, CSimSoft (2000-2009) Paraview: large data visualiztion. http://www.paraview.org/
38. D Saville O Palusinski 1986 Theory of electrophoretic separations. part i: formulation of a mathematical model AICHE J 32 2 207 214 10.1002/aic. 690320206
39. J Shim P Dutta C Ivory 2007 Modeling and simulation of IEF in 2-D microgeometries Electrophoresis 28 572 586 10.1002/elps.200600402
40. G Sommer A Hatch 2009 IEF in microfluidic devices Electrophoresis 30 742 757 10.1002/elps.200800598
41. VE Sonzogni AM Yommi NM Nigro MA Storti 2002 A parallel finite element program on a Beowulf cluster Adv Eng Softw 33 7-10 427 443 01967231 10.1016/S0965-9978(02)00059-5
42. TL Sounart JC Baygents 2007 Lubrication theory for electro-osmotic flow in a non-uniform electrolyte J Fluid Mech 576 1 139 172 1125.76018 10.1017/S0022112006003867 2308152
43. Storti MA (2005-2008) Aquiles cluster at CIMEC. http://www.cimec.org.ar/ aquiles
44. MA Storti NM Nigro RR Paz LD Dalcín 2009 Strong coupling strategy for fluid-structure interaction problems in supersonic regime via fixed point iteration J Sound Vib 320 4-5 859 877 10.1016/j.jsv.2008.09.028
45. H Svensson 1961 Isoelectric fractionation, analysis, and characterization of ampholytes in natural pH gradients. I. The differential equation of solute concentrations at steady state and its solution for simple cases Acta Chem Scand 15 325 341 10.3891/acta.chem.scand.15-0325
46. T Tezduyar Y Osawa 2000 Finite element stabilization parameters computed from element matrices and vectors Comput Method Appl M 190 3-4 411 430 0973.76057
47. T Tezduyar S Mittal S Ray R Shih 1992 Incompressible flow computations with stabilized bilinear and linear equal order interpolation velocity pressure elements Comput Method Appl M 95 221 242 0756.76048 10.1016/0045-7825(92)90141-6
48. W Thormann J Caslavska R Mosher 2007 Modeling of electroosmotic and electrophoretic mobilization in capillary and microchip isoelectric focusing J Chromatogr A 1155 2 154 163 10.1016/j.chroma.2007.01.121
49. S Tia A Herr 2009 On-chip technologies for multidimensional separations Lab Chip 9 2524 2536 10.1039/b900683b
50. Tian WC, Finehout E (2008) Microfluidics for biological applications, 1st edn. Springer, Berlin
51. Tsai WB, Hsieh CJ, Chieng CC (2005) Parallel computation of electroosmotic flow in L-shaped microchannels. In: Sixth world congress of structural and multiisciplinary optimization, pp 4971-4980
52. RT Turgeon MT Bowser 2009 Micro free-flow electrophoresis: theory and applications Anal Bioanal Chem 394 1 187 198 10.1007/s00216-009-2656-5
53. D Wu J Qin B Lin 2008 Electrophoretic separations on microfluidic chips J Chromatogr A 1184 1-2 542 559 10.1016/j.chroma.2007.11.119
54. Y Xu CX Zhang D Janasek A Manz 2005 Sub-second isoelectric focusing in free flow using a microfluidic device Lab Chip 3 224 227 10.1039/b308476k
55. S Yang J Liu DL DeVoe 2008 Optimization of sample transfer in two-dimensional microfluidic separation systems Lab Chip 8 11145 1152