Fields, Forces, and Flows in Biological Systems

Lecture Slides

Lecturer Key

AG = Alan Grodzinsky
MB = Mark Bathe

LEC #	TOPICS AND SLIDES	LECTURERS
1	Course introduction, overview, and objectives (PDF - 2.5MB)	AG
I. Chemical Subsystem
2	Introduction to random processes; Boltzmann distribution and statistical thermodynamics (PDF - 1.3MB)	MB
3	Diffusion as a random walk; Stokes-Einstein relation for diffusion coefficient (PDF - 1.5MB)	MB
4	Constitutive equations for diffusion (Fick’s Laws); Conservation of mass for a control volume; Differential form; Steady diffusion (1D); Boundary conditions (PDF)	MB
5	Diffusion and reaction; Reaction rates, order, molecularity and mechanisms; Scaling and the Damköhler number; Solution procedures (Lecture slides are not available)	MB
6	Examples of diffusion-reaction: Diffusion of a ligand through tissue with cell receptor-ligand interactions; Diffusion-reaction kinetics (PDF)	MB
7	Case study: IGF-1 diffusion-reaction within tissues and cell seeded scaffolds; binding to IGF binding proteins & cell surface receptors; experimental methods (PDF - 1.9MB)	AG
II. Electrical Subsystem
8	E-fields and transport; Maxwell’s equations (PDF - 1.2MB)	AG
9	Define electrical potential; conservation of charge; Electro-quasistatics (PDF - 6.5MB)	AG
10	Laplacian solutions via Separation of Variables; Electric field boundary conditions; Ohmic transport; Charge Relaxation; Electrical migration vs. chemical diffusive fluxes (PDF - 2.2MB)	AG
11	Electrochemical coupling; Electrical double layers; Poisson–Boltzmann Equation (PDF - 2.5MB)	AG
12	Donnan equilibrium in tissues, gels, polyelectrolyte networks (PDF - 2.0MB)	AG
13	Charge group ionization & electro-diffusion-reaction in molecular networks (PDF - 1.7MB)	AG
14	Case study: Charged protein transport in charged tissues & gels; Donnan partitioning, diffusion-reaction in extracellular matrix; experimental methods (PDF - 2.2MB)	AG
III. Mechanical Subsystem
15	Conservation of mass and momentum in fluids; convective solute transfer (PDF - 2.7MB)	MB
16	Viscous stress-strain rate relations; Navier–Stokes equations (PDF - 1.5MB)	MB
17	Low Reynolds number flows; Stokes equation; Scaling and dimensional analysis (PDF - 1.3MB)	MB
18	Newtonian, fully developed low Reynolds number flows (PDF)	MB
19	Diffusion and convection; The Peclet number; Convection-diffusion-reaction and boundary layers (PDF - 2.6MB)	MB
20	Concentration boundary layers: Fully-developed flow and transport (PDF)	MB
IV. Integrative Case Studies: Physicochemical, Mechanical, & Electrical Interactions
21	Capillary electroosmosis: Theory and experiments (PDF - 1.8MB)	AG
22	MEMs, microfluidics + electrokinetics, cells and hydrogels; (with guest lecture) (PDF - 1.5MB)	AG
23	Electrophoresis, chromatography and extracellular matrix biochemistry (PDF - 2.6MB)	AG
24	DLVO theory: Double layer repulsion and molecular interactions (proteins, DNA, GAGs) (PDF - 1.3MB)	MB
25	Porous media flows: Extracellular and intracellular (PDF - 2.1MB)	MB
26	Cell / molecular electrokinetics; review of term paper project (PDF - 2.3MB)	AG