Biophysical Methods

AEP 4700 / BIONB 4700 /
BME 5700 / VETMM 4700

Fall 2018

Biophysical Methods is an upper-division course open to seniors and graduate students that will be offered in Fall 2018.

For more information, please email the course instructor (Prof. Guillaume Lambert, ) or the course secretary/registrar (Cynthia Reynolds, ).


Course description: Overview of the diversity of modern biophysical experimental techniques used in the study of biophysical systems at the molecular, cellular, and population level.

Topics include:

  • Biology by the numbers: molecular dynamics, random motion, fundamental limits.
  • Imaging: super-resolution, multi-photon, and single-molecule microscopy.
  • Structural biology: DNA, RNA, proteins, cells, tissues.
  • Systems biology: big data, next-generation sequencing, gene regulation.
  • Synthetic biology: gene circuits, protein engineering, gene editing.

Emphasis is placed on techniques available for use on campus or likely to be encountered in cutting-edge research or industry.

Prerequisites: solid knowledge of basic physics and mathematics through sophomore level. Some knowledge of molecular and cell biology, or neurobiology.


Course instructor: Professor Guillaume Lambert.

272 Clark Hall
(607) 255-2382
.

Teaching assistant: TBD.


Course registrar: Cynthia Reynolds.

261 Clark Hall
(607) 255-0638
.

Lectures (subject to change):

Tue, Thu 2:55-4:10 PM

No lectures:
October 8 (Fall break)
November 21 (Thanksgiving Recess)
120 Physical Sciences Building

Course web site (Blackboard): Lecture slides, homework assignments, and reading assignments will be posted on blackboard. Go to the AEP 4700 site at http://www.blackboard.cornell.edu

Textbook: There is no textbook for the course, but course notes and reference notes will be posted on the blackboard web site. There is unfortunately no single book that adequately covers all of the topics that will be addressed in this course. Recommended readings may be posted on the course web site. The following books might prove useful references for particular sections:

  • Ron Milo and Rob Phillips, Cell Biology by the numbers, Garland Science, 2015.
  • Udo J. Birk, Super-Resolution Microscopy: A Practical Guide, Wiley-VCH, 2017
  • Philip Nelson, Biological Physics – Energy, Information, Life, W.H Freeman, 2013
  • Rob Phillips et al., Physical Biology of the Cell, Garland Science, 2012
  • Uri Alon, An Introduction to Systems Biology, Chapman & Hall, 2006

Lectures: Lectures are an important component of this course. Students will be responsible for the material presented in lectures. Class attendance is vital for a complete understanding of the concepts presented in this course and questions during lectures are strongly encouraged. Class participation constitutes 5% of the course grade. PowerPoint slides presented during the lectures will be handed out at the beginning of the lecture and posted on Blackboard after each lecture. Slides with additional material covered during lecture may be added. Lecture notes will be posted on Blackboard after each lecture.


Homework: Problem sets will be assigned each week on Tuesday and will be due the following Tuesday. The answer key will be posted 1 week after each problem set is due. Late homework assignments will have 10% deducted per day until the answer key is posted, after which they will not receive any credit. There is a homework box set up next to room 244 in Clark Hall for dropping off homework not turned in during class. I will drop your lowest homework score for the semester. In other words, you get one but only one “freebie”. Please use it wisely.

Examinations: There will be one preliminary exam and one team project. The exam will cover material from the lectures and assigned readings. In the team project, groups of 3 or 4 will have to write an “NIH R21”-type proposal on a particular biophysical problem that requires the application of at least 3 methods covered in class. The instructor will provide a list of subjects suitable for the proposal, but students are also welcome to consult with the instructor if they want to write the term paper on any other interdisciplinary project.

Grading:

  • Homework: 40%
  • Prelim exam: 20%
  • Team project: 40%
  • Participation: 5% Bonus

Academic Integrity: The Cornell Code of Academic Integrity will be strictly enforced. Students are encouraged to discuss homework and laboratory report questions with classmates; however, each student must prepare their own written work. Copying someone else’s homework or laboratory report is not permitted and is a clear violation of the Code of Academic Integrity.