Course Calendar:

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.

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

Final report:

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.