Here is the lecture / lab schedule for the first 5 weeks of the course. Following this, students work on research projects with a faculty mentor.
Some of the labs below are available online. Click on the lab to visit the download page.
Date |
AM Event |
PM Event: |
| Mon 9/25 | Introduction to course (Alberts) and the labs. Tour of CCD and FHL facilities. | Lecture: Review of biology (Kim) |
| Tues 9/26 | Lecture: Continuous Processes (Dawes) | Mathematica Lab 1: Introduction to Mathematica (Kim) |
| Wed 9/27 | Lecture: Biophysics: Life at low Reynolds number, Mass-Spring-Dashpot Mechanics (Alberts) | Mathematica Lab 2: Equations of motion for springs, dashpots and masses (Kim) |
| Thurs 9/28 | Lecture: Stability and Linearization (Dawes) | Mathematica Lab 3: Modeling of contractile cortex (Kim) |
| Fri 9/29 | Lecture: Enzyme Kinetics (Kim) | Mathematica Lab 4: Enzyme Kinetics (Kim) |
| Sat 9/30 | Student Presentations: Introduce yourself and present and intellectual question that thrills you (students) | Catch up on Mathematica labs |
| Mon 10/2 | Lecture: Biophysics & Brownian Motion (Alberts) | Lecture: Phase plane analysis (Dawes) |
| Tues 10/3 | Mathematica Lab 5: Searching Parameter Space (Kim) | Lecture: Phase plane analysis (Dawes) |
| Wed 10/4 | Lecture: Boltzmann's law (Alberts) and temperature dependence of enzymes & transduction (Kim) | Lecture: Phase plane analysis (Dawes) |
| Thurs 10/5 | Introduce mini-project possibilities (Kim). Lab / Problem set: Phase plane analysis (Dawes) | Guest Lecture: Biophysics approaches to networks (Tee) |
| Fri 10/6 | Begin work on Mathematica mini projects on gene networks | |
| Sat 10/7 | Continue working on mini-projects | |
| Mon 10/9 | Continue working on mini-projects | |
| Tues 10/10 | Guest Lecture: Robustness of Genetic Networks (Odell) | Continue working on mini-projects |
| Wed 10/11 | Continue working on mini-projects | |
| Thurs 10/12 | Lecture: Actin network dynamics (Littlefield) | Presentations: Mathematica mini-projects (students) |
| Fri 10/13 | Lecture: Modeling actin networks in Listeria motility (Alberts) | Lecture: Java programming with Muttons & Gluttons (Alberts) |
| Sat 10/14 | Java Lab: Programming Muttons & Gluttons (Alberts & Gile) | |
| Mon 10/16 | Java Lab: More programming (Alberts & Gile) | Lecture: Particle flux and PDEs (Dawes) |
| Tues 10/17 | Guest Lecture: Microtubules and cytokinesis (von Dassow) | Guest Lecture: Mechanics of cell division (Joe Howard from EMBL) |
| Wed 10/18 | Joe Howard Seminar | Presentations on Muttons & Gluttons (students) |
| Thurs 10/19 | Java mini-projects on contractile networks | Guest Lecture: Cortex dynamics, establishing polarity, Par proteins (Munro) |
| Fri 10/20 | Continue working on mini-projects | Lecture: Turing instability and pattern formation (Dawes) |
| Sat 10/21 | Continue working on mini-projects | |
| Mon 10/23 | Continue working on mini-projects | Lecture: Analysis of traveling waves (Dawes) |
| Tues 10/24 | Lab / problem set: PDEs and spatial processes (Dawes) | Continue working on mini-projects |
| Wed 10/25 | Continue working on mini-projects | |
| Thurs 10/26 | Continue working on mini-projects | |
| Fri 10/27 | Continue working on mini-projects | Presentations: Java mini-projects (students) |
Students begin work on research projects with faculty mentor starting Sat 10/28 |
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Half of the grade for the course is based on work done for the final research project. Students must write a report of their findings that will be bound and put into the Friday Harbor library and also give an oral presentation of their findings to the FHL community.
