# Lecture Notes

The following table presents slides for selected lectures in Parts 2 and 4, plus an introductory lecture in Part 1. Table entries for Parts 1 and 3 are retained, even though no lecture notes are available, to present the overall flow of topics during the term.

LEC # | TOPICS | DETAILS |
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Part 1: Fluids (Instructor: Prof. Scott Manalis) |
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1 |
Introduction to the course Fluid 1: Introduction to fluid flow (PDF) |
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 |

3 | Fluid 3: Conservation of momentum |
Fluid kinematics Acceleration of a fluid particle Constitutive laws (mass and momentum conservation) |

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

5 | Fluid 5: Navier-Stokes equation |
Inertial effects The Navier-Stokes equation |

6 | Fluid 6: Flows with viscous and inertial effects |
Flow regimes The Reynolds number, scaling analysis |

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

12 | Field 2: Maxwell's equations (PDF) |
Integral form of Maxwell's equations Differential form of Maxwell's equations Lorentz force law Governing equations |

13 | Quiz 1 | |

14 | Field 3: EM field for biosystems (PDF) |
Quasi-electrostatic approximation Order of magnitude of B field Justification of EQS approximation Quasielectrostatics Poisson's equation |

15 | Field 4: EM field in aqueous media (PDF) |
Dielectric constant Magnetic permeability Ion transport (Nernst-Planck equations) Charge relaxation in aqueous media |

16 | Field 5: Debye layer (PDF) |
Solving 1D Poisson's equation Derivation of Debye length Significance of Debye length Electroneutrality and charge relaxation |

17 | Field 6: Quasielectrostatics 2 (PDF) |
Poisson's and Laplace's equations Potential function Potential field of monopoles and dipoles Poisson-Boltzmann equation |

18 | Field 7: Laplace's equation 1 (PDF) |
Laplace's equation Uniqueness of the solution Laplace's equation in rectangular coordinate (electrophoresis example) will rely on separation of variables |

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

20 | Field 9: Laplace's equation 3 (PDF) | Laplace's equation in spherical coordinate (example 7.9.3) |

Part 3: Transport (Instructor: Prof. Scott Manalis) |
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21 | Transport 1 |
Diffusion Stokes-Einstein equation |

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

23 | Transport 3 |
Diffusional flux Fourier, Fick and Newton Steady-state diffusion Concentration gradients |

24 | Transport 4 |
Steady-state diffusion (cont.) Diffusion-limited reactions Binding assays Receptor ligand models Unsteady diffusion equation |

25 | Transport 5 |
Unsteady diffusion in 1D Equilibration times Diffusion lengths Use of similarity variables |

26 | Transport 6 | Electrical analogy to understanding cell surface binding |

27 | Quiz 2 | |

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

29 | Transport 8 |
Guest lecture: Prof. Kamm Transendothelial exchange |

30 | Transport 9 |
Solving the convection-diffusion equation in flow channels Measuring rate constants |

Part 4: Electrokinetics (Instructor: Prof. Jongyoon Han) |
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31 | EK1: Electrokinetic phenomena |
Debye layer (revisit) Zeta potential Electrokinetic phenomena |

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

33 | EK3: Electroosmosis 2 (PDF) |
Characteristics of electroosmotic flow Applications of electroosmotic flow |

34 | EK4: Electrophoresis 1 |
Electrophoretic mobility Theory of electrophoresis |

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

36 | EK6: Dielectrophoresis (PDF) |
Induced dipole (from part 2) C-M factor Dielectrophoretic manipulation of cells |

37 | EK7: DLVO (PDF) |
Problem of colloid stability Inter-Debye-layer interaction |

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

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