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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.

Course readings.
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 Analysis of Transport Phenomena. New York, NY: Oxford University Press, 1998. ISBN: 9780195084948.
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.