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

Assigned Readings

TY & K: Buy at Amazon 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: Buy at Amazon Probstein, R. F. Physiochemical Hydrodynamics: An Introduction. New York, NY: Wiley-Interscience, 2003. ISBN: 9780471458302.

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


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

Introduction to the course

Fluid 1: Introduction to fluid flow


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

Buy at Amazon 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


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


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

Buy at Amazon 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

Buy at Amazon 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.