PHYSICS 141: The Physics of Sensory Systems in Biology

PHYSICS 141: The Physics of Sensory Systems in Biology

Shopping Period

Prof. Samuel will hold several "drop-in" zoom meetings during Shopping Period to meet with students and discuss the course and its contents (see Zoom).  Short videos describing the academic goals and overall organization of the class will be made available (see Panopto).

Shopping Period Meetings

  • Monday, August 17th at 9 am (link)
  • Monday, August 17th at 12 pm (link)
  • Monday, August 17th at 4 pm (link)
  • Tuesday, August 18th at 9 am (link)
  • Tuesday, August 18th at 12 pm (link)

 

Reading

There is no required textbook for the course. Readings will be posted in Weekly Modules on this website (and also in the #Readings channel of our Slack website where we can engage in discussion threads about them). Much of the biology will be drawn from Sensory Transduction by Gordon Fain. Much of the physics will be drawn from Biophysics: Searching for Principles by Bill Bialek and from Random Walks in Biology by Howard Berg.

Pre-recorded lectures

All of the background physics, mathematics, and biology will be delivered in sets of pre-recorded lectures (See Panopto). Students are expected to view these pre-recorded lectures and complete the associated reading assignment before each of the scheduled class meetings.

Class meetings with Prof. Samuel

The scheduled class meetings (Tu, Th 9-10:15 AM EST) will be discussions of the material presented in the pre-recorded lectures and reading assignments.  If any students are unable to attend at 9 AM (e.g.,  because of time zone), Prof. Samuel will hold a second class meeting later on Tuesdays and Thursdays  (which will be regularly scheduled based on a student poll at the start of class).

Attendance at either the 9 AM or later meeting is mandatory. Students are free to join both. All zoom meetings will be recorded and made available on the website. Class participation is expected either live during these class meetings or through online discussions on Slack.

Section meetings with David Zimmerman, Teaching Fellow

We will schedule a weekly 1.5 h section meeting with David Zimmerman, a biophysics graduate student who is the teaching fellow for this course. The section meeting will focus on problem-solving relevant to completing the homework and programming assignments.

Student problem-solving workshops

Students are encouraged to work together to complete weekly homework and coding assignments. Slack will provide a continuous forum for exchanging ideas and discussions among students and conversing with Prof. Samuel and David Zimmerman. Students will be encouraged to schedule their own zoom meetings with one another.

We will also schedule a regular zoom weekly workshop 7-10 PM EST on Thursday evenings so that students can drop in and work together synchronously on problem sets. Prof. Samuel or David will be able to drop-in at these problem-solving workshops. 

Video and written completion of assignments

Students will individually upload their written assignments to the course website. Each problem set will also include a "concept question" that will be answered by a short self-made video (5-10 minutes).

Midterm project

Students will choose two problems from a list, and have a week to prepare written solutions and a self-made video presenting their own solutions. Midterm projects are expected to be solved individually.

Final student presentations

Throughout the course, most of our class meetings will center on discussions of classic papers in the field of sensory systems. At the end of the semester, each student will present a recently published paper of their choosing. Students will 1) write their own review-style paper; 2) prepare a video seminar that describes the importance of their chosen paper and communicates any essential physical and mathematical principles needed as background; and 3) construct their own coding project that involves either data analysis or simulation that helps to illuminate the chosen paper.

Grading

50% Video and written completion of weekly problem sets and coding assignments

20% Midterm project

20% Final student presentation

10% Class participation

 

 

 

Course Summary:

Date Details