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Single Molecule Methods (Fall 2007)

(530190) Methods in Single Molecule Biophysics, (3op/2ov) , Fall 2007

This course will give students an overview of current experimental state of the art single molecule techniques used in biophysics and elsewhere. Emphasis will be on two areas: (1) novel single molecule instrumentation and measurement methods, and (2) nano-scale molecular physics, thermodynamics, and statistical methods required to interpret measurement data.

(our lab homepage is at, and our optical tweezers research is here)

Lecturer : MSc Anders Wallin (anders.wallin “at”

Assistant : Heikki Ojala (heikki.ojala “at”

Schedule : 2007 fall, period I (weeks 36-42): 6 weeks of lectures (2h/week) and exercises/demonstrations (2h/week) + final exam.

Exercises: if you are present at the exercise you get 1 point extra. If you can’t be present email your answers to Heikki Ojala or return them in the mail-box for the Electronics-lab (Physicum 3rd floor, C-wing ). This should be done by 12 oclock on Thursdays.

1st lecture Monday 10.9.2007 12-14 in Physicum room D115

  • Introduction and Motivation
  • Single molecules vs. ensemble measurements
  • Methods: Optical Tweezers, AFM, Magnetic Tweezers, Single Molecule Fluorescence
  • Biology:
  • DNA/RNA and genetic information
  • Molecular motors: chemical energy -> mechanical energy
  • Protein folding
  • Exam material: High-Resolution, Single-Molecule Measurements of Biomolecular Motion, Greenleaf, 2007

1st Exercise, 13.9.2007 at 12-14 in room D110

  • Remember the formula for Stokes drag F = 6 * pi * eta * r * v
  • Assume water at room temperature if no information given about surrounding medium
  • Exercises 1, 2, 3 are worth 6 points, the video exercise counts double, 12 points.
  • link to video and accompanying pdf-notes:
  • the video can be viewed with RealPlayer
  • for the pdf files you need a username: nano and a password: course
  • Answers to exercise 1

2nd lecture Monday 17.9.2007 at 12-14 in room D115

2nd exercise, Thursday 20.9.2007 at 12-14 in room D110

3rd lecture Monday 24.9.2007 at 12-14 in room D115

  • Theory for polymer stretching
  • Entropic Elasticity
  • Force-extension measurements on polymers and Chain-models for polymers
  • FJC model
  • WLC model

3rd exercise Thursday 27.9.2007

4th lecture Monday 1.10.2007 at 12-14 in room D115

4th exercise Thursday 4.10.2007

5th lecture Monday 8.10.2007 at 12-14 in room D115

5th exercise 11.10.2007

Note: no lecture on Monday 15.10.2007 !

6th exercise 18.10.2007

6th lecture Monday 22.10.2007 at 12-14 in room D115

    • Review, tips for exam
    • Visit to the lab, optical tweezers demonstration


Prerequisites : undergraduate physics, MATLAB-skills for analyzing data. Grade : the course grade will be based on (40%) attendance and participation in the exercise/demo sessions and (60%) an exam at the end of the course. Books: we will not have a textbook for this course (we will use publications, powerpoint-presentations, and videos instead!), but those who find the material interesting can use these books as a reference:

Review Papers: These papers give an overview of the field.

Video Lectures

Note: If you are not able to download and view these videos we will set up a machine in the electronics lab where you can view them. Please contact me on lectures or come to the lab Physicum room C319. 1 extra exercise point for each new (good!) video-lecture on single molecule methods or single molecule biology you can find on the web!

  1. Antoine van Oijen, Xiawei Zhuang, Sunney Xie,
    • the video can be viewed with RealPlayer
    • for the pdf files you need a username: nano and a password: course
  2. Keir Neuman: Introduction to optical trapping: the single beam gradient trap.
  3. Steven B Smith: Biophysics with optical tweezers
  4. Steven B Smith: Introduction to Optical Tweezers
  5. Carlos Bustamante: Grabbing the Cat by the Tail: Packaging of DNA by Single Particles of Baceriophage phi29
  6. Steven Chu: What Can Physics Say About Life? May 2004
  7. Steven Chu: Holding on to Atoms and Molecules with Lasers: Laser Cooling – From Atomic Clocks to Watching Biomolecules Move May 2004
  8. Molecular Motors: Point Counterpoint, from the 2006 Biophysical Society Discussion Meeting.

other topics:

    • magnetic tweezers, rotary motors
    • principle, construction, examples
    • twist-stretch coupling in DNA
    • rotary molecular motors, topoisomerase
    • processivity, force-velocity relationship