This page includes a list of supplemental readings after the table of assigned readings.

## Assigned Readings

TY & K: Truskey, G. A., F. Yuan, and D. F. Katz. *Transport Phenomena in Biological Systems*. East Rutherford, NJ: Prentice Hall, 2003. ISBN: 9780130422040.

H & M: Haus, H. A., and J. R. Melcher. *Electromagnetic Fields and Energy*. Upper Saddle River, NJ: Prentice Hall, 1989. ISBN: 9780132490207. (A free online textbook.)

Probstein: Probstein, R. F. *Physiochemical Hydrodynamics: An Introduction*. New York, NY: Wiley-Interscience, 2003. ISBN: 9780471458302.

Jones: Jones, T. B. *Electromechanics of Particles*. 2nd ed. New York, NY: Cambridge University Press, 2005. ISBN: 9780521019101.

LEC # | TOPICS | DETAILS | READINGS |
---|---|---|---|

Part 1: Fluids (Instructor: Prof. Scott Manalis) | |||

1 |
Introduction to the course Fluid 1: Introduction to fluid flow |
Logistics Introduction to the course Importance of being "multilingual" Complexity of fluid properties | |

2 | Fluid 2: Drag forces and viscosity |
Fluid drag Coefficient of viscosity Newton's law of viscosity Molecular basis for viscosity Fluid rheology | TY & K: 2.5.1-2.5.3 |

3 | Fluid 3: Conservation of momentum |
Fluid kinematics Acceleration of a fluid particle Constitutive laws (mass and momentum conservation) | TY & K: 2.1-2.3 and 2.4.2 |

4 | Fluid 4: Conservation of momentum (example) |
Acceleration of a fluid particle Forces on a fluid particle Force balances | TY & K: 2.7.1 |

5 | Fluid 5: Navier-Stokes equation |
Inertial effects The Navier-Stokes equation | TY & K: 3.1-3.3 |

6 | Fluid 6: Flows with viscous and inertial effects |
Flow regimes The Reynolds number, scaling analysis |
TY & K: 3.3, 3.5, 3.6, 4.3, 4.4, and 7.3 Deen, W. "Stream Function." Section 5.9 in |

7 | Fluid 7: Viscous-dominated flows, internal flows |
Unidirectional flow Pressure driven flow (Poiseuille) | |

8 | Fluid 8: External viscous flows |
Bernoulli's equation Stream function | |

9 | Fluid 9: Porous media, poroelasticity |
Viscous flow Stoke's equation | |

10 | Fluid 10: Cellular fluid mechanics (guest lecture by Prof. Roger Kamm) | How cells sense fluid flow | |

Part 2: Fields (Instructor: Prof. Jongyoon Han) | |||

11 | Field 1: Introduction to EM theory |
Why is it important? Electric and magnetic fields for biological systems (examples) EM field for biomedical systems (examples) | |

12 | Field 2: Maxwell's equations |
Integral form of Maxwell's equations Differential form of Maxwell's equations Lorentz force law Governing equations |
H & M: 1.1, 1.2 (except example 1.2.1), 1.3 (excluding continuity), 1.4 (until example 1.4.1), 1.6 (until example 1.6.1), and 1.7 (before illustration) H & M: 2.0, 2.1, 2.3, 2.4, and 2.6 (Gauss/Stokes) |

13 | Quiz 1 | ||

14 | Field 3: EM field for biosystems |
Quasi-electrostatic approximation Order of magnitude of B field Justification of EQS approximation Quasielectrostatics Poisson's equation | H & M: 3.0, 3.2, 3.3, and 3.5 (ignore MQS parts) |

15 | Field 4: EM field in aqueous media |
Dielectric constant Magnetic permeability Ion transport (Nernst-Planck equations) Charge relaxation in aqueous media |
H & M: 6.0 through 6.4 (polarization) H & M: 9.0 (magnetization) H & M: 7.1 (ohmic conduction) H & M: 7.7 (charge relaxation) |

16 | Field 5: Debye layer |
Solving 1D Poisson's equation Derivation of Debye length Significance of Debye length Electroneutrality and charge relaxation |
Dill and Bromberg: Chapter 23 Probstein: 6.4 Himienz and Rajagopalan: 11.4 |

17 | Field 6: Quasielectrostatics 2 |
Poisson's and Laplace's equations Potential function Potential field of monopoles and dipoles Poisson-Boltzmann equation |
H & M: 4.1 H & M: 4.2 H & M: 4.3 |

18 | Field 7: Laplace's equation 1 |
Laplace's equation Uniqueness of the solution Laplace's equation in rectangular coordinate (electrophoresis example) will rely on separation of variables |
H & M: 5.1 H & M: 5.2 H & M: 5.3 H & M: 5.4 |

19 | Field 8: Laplace's equation 2 | Laplace's equation in other coordinates (solving examples using MATLAB®) | |

20 | Field 9: Laplace's equation 3 | Laplace's equation in spherical coordinate (example 7.9.3) |
H & M: 5.9 H & M: Example 7.9.3 (from section 7.9, ignore time dependence) |

Part 3: Transport (Instructor: Prof. Scott Manalis) | |||

21 | Transport 1 |
Diffusion Stokes-Einstein equation | TY & K: 6.5 and 6.6 |

22 | Transport 2 | Diffusion based analysis of DNA binding proteins | |

23 | Transport 3 |
Diffusional flux Fourier, Fick and Newton Steady-state diffusion Concentration gradients | TY & K: 6.4 and 6.7 (be prepared by reading 6.1-6.3) |

24 | Transport 4 |
Steady-state diffusion continued Diffusion-limited reactions Binding assays Receptor ligand models Unsteady diffusion equation | TY & K: 6.7, 6.8, and 6.9 |

25 | Transport 5 |
Unsteady diffusion in 1D Equilibration times Diffusion lengths Use of similarity variables | TY & K: 6.8 |

26 | Transport 6 | Electrical analogy to understanding cell surface binding | TY & K: 6.9 |

27 | Quiz 2 | ||

28 | Transport 7 |
Convection-diffusion equation Relative importance of convection and diffusion The Peclet number Solute/solvent transport Generalization to 3D | TY & K: 7.1-7.3 |

29 | Transport 8 |
Guest lecture: Prof. Kamm Transendothelial exchange | TY & K: 9.2 |

30 | Transport 9 |
Solving the convection-diffusion equation in flow channels Measuring rate constants | TY & K: 7.5.1 |

Part 4: Electrokinetics (Instructor: Prof. Jongyoon Han) | |||

31 | EK1: Electrokinetic phenomena |
Debye layer (revisit) Zeta potential Electrokinetic phenomena | Probstein: 6.4 |

32 | EK2: Electroosmosis 1 |
Electroosmotic flow Electroosmotic mobility (derivation) | Probstein: 6.5 |

33 | EK3: Electroosmosis 2 |
Characteristics of electroosmotic flow Applications of electroosmotic flow | |

34 | EK4: Electrophoresis 1 |
Electrophoretic mobility Theory of electrophoresis |
Probstein: 7.1 Probstein: 7.2 (until equation 7.2.6) |

35 | EK5: Electrophoresis 2 |
Electrophoretic mobility of various biomolecules Molecular sieving | |

36 | EK6: Dielectrophoresis |
Induced dipole (from part 2) C-M factor Dielectrophoretic manipulation of cells |
H & M: Example 7.9.3 (repeat) Jones: 2.1, 2.2 (up to section C), and 3.2 (sections A and B) |

37 | EK7: DLVO |
Problem of colloid stability Inter-Debye-layer interaction | Probstein: 8.1 |

38 | EK8: Forces |
Van der Waals forces Colloid stability theory | |

39 | EK9: Forces | Summary of the course/evaluation | |

3 hour final exam (comprehensive of the course) during the finals week |

## Supplemental Readings

### Part 1

Videos by the National Committee for Fluid Mechanics Films (NCFMF)

Quake, Stephen R., and Todd M. Squires. "Microfluidics: Fluid Physics at the Nanoliter Scale." *Reviews Of Modern Physics* 77 (July 2005): 977-1026.

Purcell, E. M. "Life at Low Reynolds Number." *American Journal of Physics* 45, no. 1 (January 1977): 3-11.

### Part 2

Deen, W. "Appendix A, Tables A-1 through A-4 (Vector Identity summary)." In *Analysis of Transport Phenomena*. New York, NY: Oxford University Press, 1998. ISBN: 9780195084948.

### Part 3

Berg, H. C. "One-dimensional Random Walks." In *Random Walks in Biology*. 2nd ed. Princeton, NJ: Princeton University Press, 1993. ISBN: 9780691000640.

Halford, Stephen E., and John F. Marko. "How do Site-specifc DNA-binding Proteins Find their Targets?" *Nucleic Acids Research* 32, no. 10 (2004): 3040-3052.

Brousseau, Louis C. "Label-Free 'Digital Detection' of Single-Molecule DNA Hybridization with a Single Electron Transistor." *J AM CHEM SOC* 128 (2006): 11346-11347.