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Class Schedule contents:

Week 1

Week 2

Week 3

Week 4

Week 5

Week 6

Week 7

Week 8

Week 9

Week 10

Week 11

 

BIOEN 485, Autumn 2009
Computational Bioengineering
 

Class Schedule

  • New material will be added each week, particularly as lecture notes, assignments, and solutions are added to the web site.
week Tuesday Lecture Thursday Lecture Lab
1

 

Oct 1: lecture 1: Introduction to Modeling (compartmental models, block diagrams, model classification)

Oct 1/2

2

Oct 6, lecture 2: Linear Systems (mechanical, fluid, chemical, electrical systems and the systems approach.

Oct 8, lecture 3: Linear Systems Analysis. (superposition principle, state-space representation and numerical solutions to higher order ODEs)
  • discussion issues 2: how do you know if an analytic or numerical solution is mathematically correct?
  • lab 1 Introduction due at 11:00 am via CollectIt,

Oct 8/9

3

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Oct 13, lecture 4 Laplace Transforms and Transfer Functions

 

Oct 15, lecture 5 Examples of Linear Systems in Bioengineering

  • Discussion Issues 3:
    • Impact of Models.
  • Lab 2 Model Building due: at 11:00 am via CollectIt,

 

Oct 15/16 lab 3

4 Oct 20, lecture 6 Steady State Analysis and Pseudo Steady State analysis
  • recommended: Khoo, Chapter 4.1 to 4.6, and 6.1 and 6.2,

Oct 22, lecture 7 Time Domain Analysis, Feedback and Stability

 

 

Oct 22/23 lab 4

5

Oct 27, lecture 8 Nonlinear Systems Analysis in 2D (Jacobian and Stability, Phase-plane response and nullclines)

  • Recommended: Khoo, Chapter 9.1 to 9.3
  • Article Discussion 4 due via CollectIt at 11:00: Gardner et al:
  • Project 1, part 1 due at 11:00 am via CollectIt (project plan).
Oct 29, lecture 9 Nonlinear Analysis cont. (Jacobian and Stability in N-dimensions, Bifurcation Theory, Sensitivity Analysis, Deterministic chaos.)
  • Lab 4 due.
  • P.G. Drazin, "Nonlinear Systems", chapter 1: "Introduction", sections 1 through 6
  • Discussion issues: from the grading rubric

Oct 29/30 lab 5 Nonlinear Systems

6

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Nov 3, lecture 10 System Identification I ( Parameter estimation, least squares, The importance of measurement error and weighting schemes)

Nov 5, lecture 11 System Identification II (Examples)

  • Lab 5 due
  • Reading assignment: none
  • Discussion Issues 6: parameter estimation

 

Nov 5/6 System Identification
7

Nov 10, lecture 12 Stochastic Chemical Reactions I (Review of probability distributions and statistics)

  • The MathWorld is a good reference for statistics. Look up probability density functions, cumulative distribution functions, mean, variance, covariance and exponential and normal distributions.
  • Project 1 due at 11:00 am via CollectIt
 Nov 12, lecture 13

Stochastic Chemical Reactions II (Gillespie Exact, Tau-leap method, Chemical Langevin Equation)

 

Nov 12/13 lab 7. Stochastic chemical reaction equations

 
8

Nov 17, lecture 14

Stochastic Processes: Brownian Dynamics I (Diffusion; Langevan Equation)

Nov 19, lecture 15 Brownian Dynamics, II (examples)

  • Lab 7 due: chemical reaction stochastic processes
Nov 19/20 lab

9

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Nov 24, lecture 16 Partial Differential Equations

No lecture -

  • Thanksgiving Holiday
  • project 2, part 1 due yesterday, Wednesday Nov 25 @ 3 pm

No lab -

  • Happy Thanksgiving!
10

Dec 1, lecture 17 Numerical Methods for Partial Differential Equations (Finite difference methods)

  • Article of the week TBA

Dec 3, lecture 18 Algorithms and Examples for PDEs

  • lab 8 due

 

Dec 3/4

  • lab 9 PDEs
11

Dec 8, lecture 19. Simulating Large Reaction Networks: Overview

Dec 10, lecture 20: Review and Course Evaluations.

Dec 11/12

  • no lab assigned this week
  • come to lab and work on final project
finals week

Tuesday, Dec 15

  • project 2 due at 5:00 pm

Wednesday, Dec 16 4:30-6:20 MGH 238.

  • project presentations.

happy winter break!

 

 

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 Last Updated:
November 17, 2009