Han, Jongyoon, and Scott Manalis, 20.330J Fields, Forces and Flows in Biological Systems, Spring 2007. (Massachusetts Institute of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed 07 Jul, 2010). License: Creative Commons BYNCSA
Fields, forces, flows and transport are fundamental to understanding the behavior of biological microsystems (bioMEMS). (Figure by Prof. Jongyoon Han.)
Course Description
This course introduces the basic driving forces for electric current, fluid flow, and mass transport, plus their application to a variety of biological systems. Basic mathematical and engineering tools will be introduced, in the context of biology and physiology. Various electrokinetic phenomena are also considered as an example of coupled nature of chemicalelectromechanical driving forces. Applications include transport in biological tissues and across membranes, manipulation of cells and biomolecules, and microfluidics.
Syllabus
This page includes a course calendar.
Course Objectives
This course develops and applies scaling laws and the methods of continuum mechanics to biomechanical phenomena over a range of length scales, from molecular to cellular to tissue or organ level. It is intended for undergraduate students who have taken a course in differential equations (18.03), an introductory course in molecular biology, and a course in transport, fluid mechanics, or electrical phenomena in cells (e.g. 6.021, 2.005, or 20.320).
Topic Outline
Part I: Mechanical Driving Forces
 Conservation of momentum
 Inviscid and viscous flows
 Convective transport
 Dimensional analysis
Part II: Electrical Driving Forces
 Maxwell's equations
 Ion transport
 E and B field in biological systems
 Electroquasistatics
 Poisson's and Laplace's equation
Part III: Chemical Driving Forces
 Conservation of mass
 Diffusion
 Steady and unsteady diffusion
 Diffusion with chemical reactions
Part IV: Electrokinetics
 Debye layer
 Zeta potential
 Electroosmosis
 Electrophoresis
 Application of electrokinetics
 Dielectrophoresis
 Debye layer repulsion forces
Textbooks and Reference Materials
Required Text (to purchase)
Truskey, G. A., F. Yuan, and D. F. Katz. Transport Phenomena in Biological Systems. East Rutherford, NJ: Prentice Hall, 2003. ISBN: 9780130422040.
Additional Texts with Assigned Readings (not required to purchase)
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, R. F. Physicochemical Hydrodynamics: An Introduction. New York, NY: WileyInterscience, 2003. ISBN: 9780471458302.
Jones, T. B. Electromechanics of Particles. 2nd ed. New York, NY: Cambridge University Press, 2005. ISBN: 9780521019101.
Other Useful References
Bird, R. B., E. N. Lightfoot, and W. E. Stewart. Transport Phenomena. New York, NY: Wiley, 2006. ISBN: 9780470115398.
Weiss, T. F. Cellular Biophysics  Volume 1: Transport. Cambridge, MA: MIT Press, 1996. ISBN: 9780262231831.
Morgan, H., and H. Green. AC Electrokinetics: Colloids and Nanoparticles. Baldock, UK: Research Studies Press, 2002. ISBN: 9780863802553.
Hiemenz, P. C., and R. Rajagopalan. Principles of Colloid and Surface Chemistry. New York, NY: Marcel Dekker, 1997. ISBN: 9780824793975.
Dill, K., and S. Bromberg. Molecular Driving Forces. New York: Garland Press, 2002. ISBN: 9780815320517.
Class Structure
20.330/2.793/6.023 will be taught in lecture format (3 hours/week), but with liberal use of class examples to link the course material with various biological issues. Readings will be drawn from a variety of primary and text sources as indicated in the lecture schedule.
Optional tutorials will also be scheduled to review mathematical concepts and other tools (Comsol FEMLAB) needed in this course.
Weekly homework problem sets will be assigned each week to be handed in and graded.
Office hours by the TA will be scheduled to help you in exams and homeworks.
There will be two inclass midterm quizzes (1 hour long), and a comprehensive final exam (3 hours long) at the end of the term.
Term Grade
The term grade will be a weighted average of exams, term paper and homework grades. The weighting distribution will be:
Grading criteria.
ACTIVITIES

PERCENTAGES

Two quizzes (20% each)

40%

A comprehensive final exam

30%

Homeworks

30%

Homework
Homework is intended to show you how well you are progressing in learning the course material. You are encouraged to seek advice from TAs and collaborate with other students to work through homework problems. However, the work that is turned in must be your own. It is a good practice to note the collaborator in your work if there has been any.
Homework is due at the end of the lecture (11 am), on the stated due date. Solutions will be provided online after the due date and time.
We will not accept late homework for any reason. Instead, we will not use 2 lowest homework grades (out of 9 total) for the calculation of the term homework grade (30%). Students are encouraged to use this to their benefit, to accommodate special situations such as interview travel/illness.
Midterm Quizzes and Final Exam
There are two inclass (1 hour) closedbook midterm quizzes scheduled for the term. Please note the schedule for the exam dates. There will also be a closedbook, threehourlong, comprehensive final exam during the finals week. The final exam will cover the whole course content.
Exam problems will be similar (in terms of difficulty) to homework problems, and if one can work all the homework problems without looking at notes one should be able to solve the exam problems as well.
Makeup exams will only be allowed for excused absence (by Dean's office) and if arranged at least 2 weeks in advance. Students must sign an honor statement to take a makeup exam. Exams missed due to an excused illness and other reasons excusable by Dean's office will be dropped and the term grade will be calculated based on the remaining exams and homework.
Calendar
The table below provides information on the course's lecture (L) and tutorials (T) sessions.
Course calendar.
SES #

TOPICS

DETAILS

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

L1

Introduction to the course
Fluid 1: Introduction to fluid flow

Logistics
Introduction to the course
Importance of being "multilingual"
Complexity of fluid properties

T1

Curl and divergence


L2

Fluid 2: Drag forces and viscosity

Fluid drag
Coefficient of viscosity
Newton's law of viscosity
Molecular basis for viscosity
Fluid rheology

L3

Fluid 3: Conservation of momentum

Fluid kinematics
Acceleration of a fluid particle
Constitutive laws (mass and momentum conservation)

L4

Fluid 4: Conservation of momentum (example)

Acceleration of a fluid particle
Forces on a fluid particle
Force balances

L5

Fluid 5: NavierStokes equation

Inertial effects
The NavierStokes equation

L6

Fluid 6: Flows with viscous and inertial effects

Flow regimes
The Reynolds number, scaling analysis

L7

Fluid 7: Viscousdominated flows, internal flows

Unidirectional flow
Pressure driven flow (Poiseuille)

L8

Fluid 8: External viscous flows

Bernoulli's equation
Stream function

L9

Fluid 9: Porous media, poroelasticity

Viscous flow
Stoke's equation

L10

Fluid 10: Cellular fluid mechanics (guest lecture by Prof. Roger Kamm)

How cells sense fluid flow

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

L11

Field 1: Introduction to EM theory

Why is it important?
Electric and magnetic fields for biological systems (examples)
EM field for biomedical systems (examples)

L12

Field 2: Maxwell's equations

Integral form of Maxwell's equations
Differential form of Maxwell's equations
Lorentz force law
Governing equations

L13

Quiz 1


L14

Field 3: EM field for biosystems

Quasielectrostatic approximation
Order of magnitude of B field
Justification of EQS approximation
Quasielectrostatics
Poisson's equation

L15

Field 4: EM field in aqueous media

Dielectric constant
Magnetic permeability
Ion transport (NernstPlanck equations)
Charge relaxation in aqueous media

L16

Field 5: Debye layer

Solving 1D Poisson's equation
Derivation of Debye length
Significance of Debye length
Electroneutrality and charge relaxation

T2

FEMLAB Demo


L17

Field 6: Quasielectrostatics 2

Poisson's and Laplace's equations
Potential function
Potential field of monopoles and dipoles
PoissonBoltzmann equation

L18

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

L19

Field 8: Laplace's equation 2

Laplace's equation in other coordinates (solving examples using MATLAB®)

L20

Field 9: Laplace's equation 3

Laplace's equation in spherical coordinate (example 7.9.3)

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

L21

Transport 1

Diffusion
StokesEinstein equation

L22

Transport 2

Diffusion based analysis of DNA binding proteins

L23

Transport 3

Diffusional flux
Fourier, Fick and Newton
Steadystate diffusion
Concentration gradients

L24

Transport 4

Steadystate diffusion (cont.)
Diffusionlimited reactions
Binding assays
Receptor ligand models
Unsteady diffusion equation

L25

Transport 5

Unsteady diffusion in 1D
Equilibration times
Diffusion lengths
Use of similarity variables

L26

Transport 6

Electrical analogy to understanding cell surface binding

L27

Quiz 2


L28

Transport 7

Convectiondiffusion equation
Relative importance of convection and diffusion
The Peclet number
Solute/solvent transport
Generalization to 3D

L29

Transport 8

Guest lecture: Prof. Kamm
Transendothelial exchange

L30

Transport 9

Solving the convectiondiffusion equation in flow channels
Measuring rate constants

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

L31

EK1: Electrokinetic phenomena

Debye layer (revisit)
Zeta potential
Electrokinetic phenomena

L32

EK2: Electroosmosis 1

Electroosmotic flow
Electroosmotic mobility (derivation)

L33

EK3: Electroosmosis 2

Characteristics of electroosmotic flow
Applications of electroosmotic flow

L34

EK4: Electrophoresis 1

Electrophoretic mobility
Theory of electrophoresis

L35

EK5: Electrophoresis 2

Electrophoretic mobility of various biomolecules
Molecular sieving

L36

EK6: Dielectrophoresis

Induced dipole (from part 2)
CM factor
Dielectrophoretic manipulation of cells

L37

EK7: DLVO

Problem of colloid stability
InterDebyelayer interaction

L38

EK8: Forces

Van der Waals forces
Colloid stability theory

L39

EK9: Forces

Summary of the course/evaluation

