8.592J Organization - Spring 2018

General Information

Course Catalog description:

8.592J/HST.452J: Statistical Physics in Biology


Prerequisites: Statistical Mechanics (8.333).
Units: 3-0-9
Lectures: TR 9:30-11:00 am ( 4-265), First lecture on Tuesday, February 6.

Use of the Web

The URL for the course home page is http://web.mit.edu/8.592/www. Students should check this page frequently for updates.

The distribution of all documents (course schedule, lecture notes, assignments, and other handouts and announcements) will be done mostly using the World-Wide-Web.

Grades will be posted on the web using student aliases to maintain confidentiality. Aliases should be chosen by students when checking in online at the start of term.

You can also send your comments anonymously using the provided online form (Be constructive!). Discussions of general interest will be posted.

Browsing/Reading material:

The presentation of material does not follow a specific textbooks for this course.

However, the following books are set aside for the course at the main MIT library, and the Physics Reading Room 4-332:

Molecular Biology of the Cell (3rd edition), by Alberts et al. is a standard reference to modern biology.
Biological sequence analysis, by Durbin et al . describes some of the standard computational methods used in bioinformatics.
Unraveling DNA by Frank-Kamenetskii, presents several relevant topics in a way that should appeal to physical scientists.
Molecular Biology of the Gene, by Watson et al. is another standard reference to modern biology.
Biological Physics, by Philip Nelson is a textbook by a statistical physicist.
Physical Biology of the Cell, by Rob Philips, Jane Konev, and Julie Theriot.
Mechanics of Motor Proteins and the Cytoskeleton, by Jonathan Howard.
Protein Physics, by Finkelstein and Ptitsyn.

There are many excellent resources on the web. Here are a few examples- additional ones will be posted with the lectures.

A course by Prof. Goldenfeld on Statistical Physics of Biological Information and Complexity

Kimball's online biology textbook

(Feel free to recommend any links that you find useful, and I'll post them.)

Assignments

The homework assignments are an important part of this course, and the overall average homework score will count for 80% of the final grade. You may consult with classmates in "study groups," as long as you write out your own answers.

The complete schedule of assignments (there will be 8) with due dates is available online. Hyperlinks to the actual problem sets and solutions will be created as the term progresses. Problem sets are due by 5:00 pm on the due date. They can to be turned in lectures, in bins setup by the department, or by arrangement with the TA.

No problem sets will be accepted after the solutions have been posted. Late problem sets (before solutions are posted) may be accepted (with legitimate excuses) for a reduced grade as the discretion of the instructors.

Occasionally, there are problems marked as optional in the problem sets. If attempted, these problems will be graded as other problems, and their score added to the total. The overall grade for the course has a 80% contribution from the (required) problem sets. Thus, perfect scores on all the non-optional problems leads to the maximal grade of 80 from the problem sets. The optional problems provide a chance to reach the 80%-score for the problem sets, even when some of the required problems are not correct.

A Final Project will count for 20% of the final grade, and should be planned in consultation with the course staff by the end of March. If you need help with the writing aspects of the Final Project, the following may be relevant: "The WCC at MIT (Writing and Communication Center) offers free one-on-one professional advice from communication experts (MIT lecturers who have advanced degrees and who are all are published writers). The WCC works with undergraduate and graduate students and with post-docs and faculty. The WCC helps you strategize about all types of academic and professional writing as well as about all aspects of oral presentations (including practicing presentations & designing slides). No matter what department or discipline you are in, we help you think your way more deeply into your topic, help you see new implications in your data, research and ideas. The WCC also helps with all English as Second Language issues, from writing and grammar to pronunciation and conversation practice. The WCC is located in Kendall Square (E39-115, 55 Hayward Street, in the same building that houses Rebecca’s Cafe). To register with our online scheduler and to make appointments, go to https://mit.mywconline.com/. To access the WCC’s many pages of advice about writing and oral presentations, go to http://cmsw.mit.edu/writing-and-communication-center/ . The Center’s core hours are Monday-Friday, 9:00 a.m.-6:00 p.m.; evening hours vary by semester–check the online scheduler for up-to-date hours."

Grading

Final grades will be determined from:

Your final letter grade will reflect our best attempt to evaluate objectively your performance in the course:

A: Exceptionally good performance, demonstrating a superior understanding of the subject matter, a foundation of extensive knowledge, and a skillful use of concepts and/or materials.

B: Good performance, demonstrating capacity to use the appropriate concepts, a good understanding of the subject matter, and an ability to handle the problems and materials encountered in the subject.

C: Adequate performance, demonstrating an adequate understanding of the subject matter, an ability to handle relatively simple problems, and adequate preparation for moving on to more advanced work in the field.

D: Minimally acceptable performance, demonstrating at least partial familiarity with the subject matter and some capacity to deal with relatively simple problems, but also demonstrating deficiencies serious enough to make it inadvisable to proceed further in the field without additional work.

F: Failed. This grade also signifies that the student must repeat the subject to receive credit.

--From the MIT Regulations of the Faculty

In accord with MIT Rules and Regulations of the Faculty section 2.62, the Physics Department does not grade on a curve. Students are assessed individually, and there is no pre-determined grade spread in any subject. Consistent with this, after Drop Date, students who remain in a class are not in jeopardy of seeing their grades change due to the change in class composition.

Please note the availability of the following resources in case of need:

Student Support Services

If you are dealing with a personal or medical issue that is impacting your ability to attend class, complete work, or take an exam, please discuss this with Student Support Services (S3). The deans in S3 will verify your situation, and then discuss with you how to address the missed work. Students will not be excused from coursework without verification from Student Support Services. You may consult with Student Support Services in 5-104 or at 617-253-4861. Also, S3 has walk-in hours Monday-Friday 9:00-10:00am.

Student Disability Services

MIT is committed to the principle of equal access. Students who need disability accommodations are encouraged to speak with Kathleen Monagle, Associate Dean, prior to or early in the semester so that accommodation requests can be evaluated and addressed in a timely fashion. Even if you are not planning to use accommodations, it is recommended that you meet with SDS staff to familiarize yourself with the services and resources of the office. You may also consult with Student Disability Services in 5-104 or at 617-253-1674. If you have already been approved for accommodations, please contact me early in the semester so that we can work together to get your accommodation logistics in place.


8.592 Organization - last update 2/1/18 by M. Kardar