This Course at MIT

This Course at MIT pages provide context for how the course materials published on OCW were used at MIT. They are part of the OCW Educator initiative, which seeks to enhance the value of OCW for educators.

Course Overview

This page focuses on the course 8.592J/HST.452J Statistical Physics in Biology as it was taught by Professor Mehran Kardar and Professor Leonid Mirny in Spring 2011.

This is a graduate-level course primarily geared toward physics graduate students. The course surveys problems at the interface of statistical physics and modern biology. Homework plays an important role in this course.

Course Outcomes

Course Goals for Students

Two communities are served by this course. For physics graduate students not specializing in biophysics, the goal is for them to gain familiarity with topics outside their primary research area(s). For students specializing in biophysics, the goal is for them to learn tools and concepts relevant to their thesis and research.

 

Curriculum Information

Prerequisites

Requirements Satisfied

Offered

  • Every other spring semester

The Classroom

  • Photo of a classroom with long tables arranged with chairs so that they face the four chalkboard panels in the front of the room.

    This course was taught in a medium-sized classroom equipped with chalkboards and a projector.

 

Student Information

27 students took this course in Spring 2011.

Breakdown by Year

Roughly 75% graduate students, 25% undergraduate juniors and seniors.

Breakdown by Major

Mostly physics majors with some participants from Health Sciences and Technology, chemical engineering, and other departments at MIT, as well as Harvard University students.

Typical Student Background

The primary target is graduate students in physics. It is assumed that the students are familiar with basic tools of statistical physics (e.g., probability, ensembles, partition functions, ...), but no familiarity with biology is assumed. Web links to resources describing the biological context are provided.

 
 

How Student Time Was Spent

During an average week, students were expected to spend 12 hours on the course, roughly divided as follows:

Lecture

3 hours per week
  • Met twice a week for 1.5 hours per session
  • Much of the course material was distributed through the web, and web resources were also used during class to illustrate various points.
  • Class typically began with about half an hour spent on introducing a topic through web links and focusing on a conceptual or computational problem.
  • The remaining hour of class was typically spent on carrying out relevant calculations on the chalkboard.
 

Out of Class

9 hours per week
 

Semester Breakdown

WEEK M T W Th F
1 No classes throughout MIT. Lecture session. No session scheduled. Lecture session. No session scheduled.
2 No session scheduled. Lecture session. No session scheduled. Lecture session. No session scheduled.
3 No classes throughout MIT. No session scheduled. No session scheduled. Lecture session; homework due. No session scheduled.
4 No session scheduled. Lecture session. No session scheduled. Lecture session. No session scheduled.
5 No session scheduled. Lecture session. No session scheduled. Lecture session; homework due. No session scheduled.
6 No session scheduled. Lecture session. No session scheduled. Lecture session. No session scheduled.
7 No session scheduled. Lecture session; homework due. No session scheduled. Lecture session. No session scheduled.
8 No classes throughout MIT. No classes throughout MIT. No classes throughout MIT. No classes throughout MIT. No classes throughout MIT.
9 No session scheduled. Lecture session; homework due. No session scheduled. Lecture session. No session scheduled.
10 No session scheduled. Lecture session. No session scheduled. Lecture session; homework due. No session scheduled.
11 No classes throughout MIT. No classes throughout MIT. No session scheduled. Lecture session. No session scheduled.
12 No session scheduled. Lecture session; homework due. No session scheduled. Lecture session. No session scheduled.
13 No session scheduled. Lecture session. No session scheduled. Lecture session; homework due. No session scheduled.
14 No session scheduled. Lecture session. No session scheduled. Lecture session. Lecture session; homework due.
15 No session scheduled. Lecture session. No session scheduled. Lecture session; final project due. No session scheduled.
16 No classes throughout MIT. No classes throughout MIT. No classes throughout MIT. No classes throughout MIT. No classes throughout MIT.
Displays the color and pattern used on the preceding table to indicate dates when classes are not held at MIT. No classes throughout MIT
Displays the color used on the preceding table to indicate dates when lecture sessions are held. Lecture
Displays the color used on the preceding table to indicate dates when final projects are due. Final project due date
Displays the color used on the preceding table to indicate dates when no Lecture session is scheduled. No Lecture session scheduled
Displays the symbol used on the preceding table which indicates dates when assignments are due. Homework due date
 
 

Instructor Insights

Below, Professor Mehran Kardar describes various aspects of how he taught 8.592J Statistical Physics in Biology.

Using the Internet as a Key Resource for Fast-Developing Fields

Unlike core physics topics, biological knowledge is constantly changing. Rather than relying on a textbook, we relied on material on the web to present the most recent developments to the students. We particularly relied on the web for certain topics. For example, sequence comparison tools (BLAST) and protein structure characteristics were demonstrated through publicly available programs and databases. Other publicly available applets were important for demonstrating relevant concepts. Links to all these resources are available in the posted materials.

Preparing Afresh for Each Semester

We did not rely on previously presented materials, but rather prepared each lecture fresh. The purpose of the course is to introduce diverse topics where tools/concepts from statistical physics have been used in biology. Since this is an active research area with new topics and applications introduced regularly, we tried to keep up by updating the syllabus.

To this end, the co-lecturers got together prior to the semester to make up an overall plan of organizing the topics and problem sets.

Finally, prior to each class, I reviewed the material to be posted on the web (including lecture notes) and went over the entirety of the lecture.

 

Course Team Roles

Lecturers (Professor Mehran Kardar and Professor Leonid Mirny)

The course was co-taught by two lecturers alternating between topics with more of a biophysics, or statistical physics, focus.

Teaching Assistant

A teaching assistant was charged with grading the eight problem sets. There were no recitations or exercise classes.