| 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
<-- RETURN TO TOP |
Oct 13, lecture 4 Laplace Transforms and Transfer Functions
|
Oct 15, lecture 5 Examples of Linear Systems in Bioengineering
- Discussion Issues 3:
- 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
- Lab 3 Transfer functions due: at 11:00 am via CollectIt,
- Discussion: steady state and pseudo steady state.
|
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
<-- RETURN TO TOP |
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 (issues with spanning time and length scales, Ermak Algorithm)
|
Nov 19/20 lab
- Lab 7 due: chemical reaction stochastic processes
- Lab 8 posted: diffusive stochastic processes
|
9
<-- RETURN TO TOP |
Nov 24, lecture 16 Partial Differential Equations |
No lecture -
Thanksgiving Holiday |
No lab -
Thanksgiving Holiday |
| 10 |
Dec 1, lecture 17 Numerical Methods for Partial Differential Equations (Finite difference methods) |
Dec 3, lecture 18 Algorithms and Examples for PDEs
|
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 work on final project |
| finals week |
Tuesday, Dec 15
project 2 due at 5:00 pm |
good luck on exams!
|
happy winter break! |