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Single Molecule Methods (Fall 2011)

(530190) Methods in Single Molecule Biophysics, (3op) , Fall 2011


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. The course was lectured previously in 2007 (old web page)

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

Assistant : MSc Kalle Hanhijärvi (kalle.hanhijarvi “at”

Schedule : Fall 2011, period II. Lectures: Tue 14-16, in D116. Exercises: Wed 12-14, in D116.

First lecture: Tue 1.11.2011 14-16, D116, Physicum


Lecture 1, 1.11. PDF

– Introduction
– Length scales in single molecule biophysics (
– Single molecule vs. ensemble measurements (A.E. Knight: Introduction: The “Single Molecule” Paradigm)
– Protein folding (Protein Folding Problem)

Lecture 2, 2.11. (NB!) PDF

Howard’s Book, chapter 2
– Forces on the micro-scale
– Mass, stiffness, damping, time-constants
– Langevin equation, diffusion simulations (simple diffusion simulation: simple diffusion simulation)

Lecture 3, 8.11. PDF

– Optical trapping (idea, experiment-geometry, example experiments)
– Force-range, position-detection range
– Basics of ray-optics and rayleigh regime theory
– Brownian dynamics (power-spectrum relation to Fourier transform). Derive power-spectrum
for free diffusion, trapped massless particle.

PSD examples: PDF

Reading for Lecture 3: Greenleaf et al. (2007)

Lecture 4, 15.11. PDF

Chain models for polymers(DNA)
– Freely Jointed Chain (FJC). 1D, 2D
– Worm-Like Chain (WLC)

FJC simulations:

Lecture 5, 22.11.

– Kramers-Bell “energy-landscape” model for RNA-hairpins.

Material:  Bustamante et al.  “Mechanical Processes in Biochemistry”
See/understand especially Fig 1 and Fig 2.

Slides/Talk by Felix Ritort ca. pages 13 – 34 (this talk has much advanced material which was not covered on the lecture!)

Lecture 6, 29.11.

– Fluorescence and super-resolution microscopy
Material: L. Schermelleh et al. “A guide to super-resolution fluorescence microscopy”
Video: “Nature Methods: Method of the Year 2008”

Lecture 7, 13.12.

– We will go through the papers you have selected for the home-exam.

More lecture material


  • Exercise 1,  9.11., PDF, Solutions
  • Exercise 2, 16.11., PDF (NB, corrected version!), Solutions
  • Exercise 3, 23.11., PDF, Solutions
  • Exercise 4, 30.11., PDF, Solutions, data files:


Everyone writes a brief review of a recent scientific publication relevant to the course. Length 2-5 pages. In finnish, swedish, or english. Submit by 31.12.2011. Take each figure and equation from the paper and explain it in sufficient detail so that a fellow student who has not taken this course can understand what is going on.

Possible papers:

– Rief et al. “The Complex Folding Network of Single Calmodulin Molecules”
– Smith et al. “The bacteriophage phi29 portal motor can package DNA against a large internal force”, Supplement
-Bouchiat et al. “Estimating the Persistence Length of a Worm-Like Chain Molecule from Force-Extension Measurements”
– Greenleaf, et al. “Direct Observation of Hierarchical Folding in Single Riboswitch Aptamers”
– Eva Rittweger, Kyu Young Han, Scott E. Irvine, Christian Eggeling, Stefan W. Hell (2009). “STED microscopy reveals crystal colour centres with nanometric Resolution.”. Nature Photonics 3 (3): 144–147.  10.1038/nphoton.2009.2.
– Michael J Rust, Mark Bates & Xiaowei Zhuang, Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM), Nature Methods3, 793 – 796 (2006) ,  doi:10.1038/nmeth929
– Keir C. Neuman and Steven M. Block, “Optical trapping”, Rev. Sci. Instrum. 75, 2787 (2004); doi:10.1063/1.1785844


Updated: 29.11.2011