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: WileyInterscience, 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: 2.5.12.5.3 
3  Fluid 3: Conservation of momentum 
Fluid kinematics Acceleration of a fluid particle Constitutive laws (mass and momentum conservation) 
TY & K: 2.12.3 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: NavierStokes equation 
Inertial effects The NavierStokes equation 
TY & K: 3.13.3 
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 Analysis of Transport Phenomena. New York, NY: Oxford University Press, 1998. ISBN: 9780195084948. 
7  Fluid 7: Viscousdominated 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 
Quasielectrostatic 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 (NernstPlanck 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 PoissonBoltzmann 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 StokesEinstein 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 Steadystate diffusion Concentration gradients 
TY & K: 6.4 and 6.7 (be prepared by reading 6.16.3) 
24  Transport 4 
Steadystate diffusion continued Diffusionlimited 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 
Convectiondiffusion equation Relative importance of convection and diffusion The Peclet number Solute/solvent transport Generalization to 3D 
TY & K: 7.17.3 
29  Transport 8 
Guest lecture: Prof. Kamm Transendothelial exchange 
TY & K: 9.2 
30  Transport 9 
Solving the convectiondiffusion 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) CM 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 InterDebyelayer 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): 9771026.
Purcell, E. M. “Life at Low Reynolds Number.” American Journal of Physics 45, no. 1 (January 1977): 311.
Part 2
Deen, W. “Appendix A, Tables A1 through A4 (Vector Identity summary).” In Analysis of Transport Phenomena. New York, NY: Oxford University Press, 1998. ISBN: 9780195084948.
Part 3
Berg, H. C. “Onedimensional 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 Sitespecifc DNAbinding Proteins Find their Targets?” Nucleic Acids Research 32, no. 10 (2004): 30403052.
Brousseau, Louis C. “LabelFree ‘Digital Detection’ of SingleMolecule DNA Hybridization with a Single Electron Transistor.” J AM CHEM SOC 128 (2006): 1134611347.