This course will provide an overview of the physics and mathematical description of soft matter as well as living systems. The subjects and approaches, from phenomenology to detailed calculations, will span the range of length scales from molecular to ecological. We will approach the topic from the forces of interaction at the molecular level and go upwards through the length scales to discuss complex, living materials.
The material is for your private use. Please do not distribute. PDFs of articles, in case we have them, are accessible via links below.
PRELIMINARY Lecture notes
You can get a pdf of the preliminary lecture notes (now with literature list) here. These will be updated constantly and will contain a significant amount of mistakes - so please let us know if you find them. Please help us and send an email with your corrections to Ray (reg53) or me (ufk20) .
Physics example classes
Small Lecture Theater, Cavendish Lab
1: 3/11 10:00-11:00
2: 10/11 10:00-11:00
3: 24/11 10:00-11:00
4: 01/12 10:00-11:00
You can download the first MATH question sheet here.
Numerical solutions for the first MATH can be found here.
You can download the second MATH question sheet here.
You can download the PHYSICS question sheet here.
Example solutions 00-08 can be found here.
Example solutions 09-14 can be found here.
Here you find an example for a brief question answer.
Literature/further reading for topics
Below you find a list of books and topics which I recommend for reading. Where, following the book title, a specific chapter is given this means you can find there material presented/discussed in the lectures.
When I only give the title of the book this is for general reference only and intended for further background reading. Since the course extensively uses original research papers as sources these
are given as pdfs and should be read UNLESS marked as "advanced". Especially important topics will be marked with (*). Please read/have a look at the papers in these sections which are not marked as advanced.
for diffusion, random walks, nice introduction: H. C. Berg "Random Walks in Biology"
great book for life sciences from physics point of view: Schrodinger "What is life"
historical perspective: M. Haw "Middle World"
(*) Optical Tweezers
background for Langevin equation and harmonic oscillators: Chaikin, Lubensky "Principles of Condensed Matter Physics" chapter 7.5
more concise on Langevin and fluctuation dissipation: Dill, Bromber "Molecular Driving Forces" chapter 18
(*) comprehensive overview over most state of the art techniques: Neuman, Block, "Optical Trapping", Review of Scientific Instruments (2004) pdf
very good paper about power spectra: Gittes, Schmidt, "Signals and Noise in Micromechanical Measurements" (1998) pdf
(*) good review about single molecule studies: Bustamante et al. "Ten Years of Tension: Single Molecule DNA mechanics" Nature (2003) pdf
nice overview: Ashkin, "Optical trapping and manipulation of neutral particles using lasers" PNAS (1997) pdf
(*) advanced paper: Bustamante et al. "Mechanical Processes in Biochemistry" (2004) pdf
laser tracking: Keyser et al. "Optical tweezers for force measurements on DNA in nanopores" Review of Scientific Instruments (2006) pdf
video tracking: Otto et al. "Real-time Particle Tracking at 10,000 fps using Optical Fiber Illumination" Optics Express (2010) pdf
(*) advanced paper: Peterman, Gittes, Schmidt "Laser-induced heating in optical traps" Biophys. J. (2003) pdf
Padgett group in Glasgow has a lot of fun movies about optical tweezers link
More on microscopy and the basics there can be found at Olympus website link
or even more from Nikon with nice Java applets link
Optical tweezers TETRIS link
(*) Magnetic Tweezers and Super-coiled DNA
(*) Magnetic tweezers, technique: Gosse and Croquette "Magnetic Tweezers: Micromanipulation and Force Measurements at the Molecular Level", Biophys. J. (2002) pdf
(*) polymer dynamics: Crut et al. "Fast dynamics of supercoiled DNA revealed
by single-molecule experiments" PNAS (2007) pdf
friction in proteins: Koster et al. "Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB" Nature (2005) pdf
one of the first papers using single molecule techniques to clarify how a drug molecule works: Koster et al. "Antitumour drugs impede DNA uncoiling by topoisomerase I" Nature (2007) pdf
P-DNA with magnetic tweezers: Allemand et al. "Stretched and overwound DNA forms a Pauling-like structure with exposed bases" PNAS (1998) pdf
(*) DNA, Force extension, FJC, ...
DNA structure: Drew and Calladine "Understanding DNA"
Force extension: Nelson "Biological Physics", chapter 9
Force extension: Phillips et al. "Physical Biology of the Cell", Chapter 8 and 10
(*) seminal paper: Wang et al. "Stretching DNA with Optical Tweezers", Biophysical Journal (1997) pdf
(*) seminal paper, refined WLC: Bouchiat et al. "Estimating the Persistence Length of a Worm-Like Chain Molecule from Force-Extension Measurements" Biophys. J. (1999) pdf
(*) dependence of persistence length on ionic conditions: Baumann et al. "Ionic effects on the elasticity of single DNA molecules" PNAS (1997) pdf
Atomic Force Microscopy
background on trapping on surfaces: Bustamante & Rivetti, "Visualizing protein-nucleic acid interactions on a large scale with the scanning force microscope" Ann. Rev. Biophy. (1996) pdf
written by two main researchers in the field: Engel & Muller, "Observing single biomolecules at work with the atomic force microscope" Nature Structural Biology (2000) pdf
seminal paper: Hansma et al. "Reproducible Imaging and Dissection of Plasmid DNA Under Liquid with the Atomic ForceMicroscope" Science (1992) pdf
technical recipes: Muller & Engel, "Atomic force microscopy and spectroscopy of native membrane proteins" Nature Methods (2007) pdf
one example for filming proteins with AFM: Moreno-Herrero, et al. "Mesoscale conformational changes in the DNA-repair complex Rad50/Mre11/Nbs1 upon binding DNA", Nature 2005 pdf
(*) Proteins, folding and unfolding
protein structure and relevance: Alberts, et al., "Molecular Biology of the Cell"
protein structure and relevance: Lodish, Berk, et al., "Molecular Cell Biology"
protein folding: Fersht, "Structure and Mechanism in Protein Science", Chapter 19
first passage time, q1: Phillips et al. "Physical Biology of the cell", Chapter 16
folding funnel: Leopold, Montal, Onuchic, "Protein folding funnels, A kinetic approach to the sequence-structure relationship", PNAS 1992 pdf
(*) forced unfolding of proteins: Rief et al. "Reversible Unfolding of Individual Titin Domains by AFM", Science 276 1109 (1997) pdf
(*) Levinthal paradox revisited: Zwanzig, Szabo, Bagchi "Levinthal's paradox", PNAS 1992 pdf
(*) concise treatise of all major phenomena: Hunter et al., "Measurement and interpretation of electrokinetic phenomena", J. Coll. Interface Sci. (2007) pdf
technical development paper: Otto, et al. "Optical tweezers with 2.5 kHz bandwidth video detection for single-colloid electrophoresis" Rev. Sci. Instr. (2008) pdf
paper discussed in q7: Semenov, et al., "Single colloid electrophoresis" J. Coll. Interface Sci. (2009) pdf
Santiago Lab at Stanford for imaging of flows in channels link
(*) Entropic Trapping
nanotechnology: Turner, Cabodi, Craighead "Confinement-Induced Entropic Recoil of Single DNA Molecules in a Nanofluidic Structure" Phys. Rev. Lett. (2002) pdf
in gels: Liu, Li, Asher "Entropic trapping of macromolecules by mesoscopic periodic voids in a polymer hydrogel" Nature (1999) pdf
general polymer physics and dynamics: Rubinstein "Polymer Physics", chapters 7-9
for reptation and relaxation times: Strobl "The Physics of Polymers", Chapter 3,8
modern perspective - practical, nice: Viovy, "Electrophoresis of DNA and other polyelectrolytes: Physical mechanisms", Rev. Mod. Phys. (2000) pdf
basic ideas, solution for q11: Zimm and Levene, "Problems and prospects in the theory of gel electrophoresis of DNA" Qart. Rev. Biophys (1992) pdf
very biological perspective: Hille, "Ion Channels of Excitable Membranes", Chapter 11
basic intro: Berg "Random walks in biology", chapter 1-4
(*) forces in nanopores 1: Keyser, van Dorp, Lemay, "Tether forces in DNA electrophoresis", Chem. Soc. Rev. (2010) pdf
(*) nice overview: Dekker "Solid-state Nanopores", Nature Nanotechnology (2007) pdf
seminal paper: Kasianowicz et al. "Characterization of individual polynucleotide molecules using a membrane channel" pdf
advanced seminal paper, original nanopore fabrication: Li et al. "Ion-beam sculpting at nanometre length scales" Nature (2001) pdf
seminal paper: Li et al. "DNA molecules and configurations in a solidstate nanopore microscope" Nature Materials (2003) pdf
(*) fast translocation: Storm et al. "Fast DNA Translocation through a Solid-State Nanopore" Nano Letters (2005) pdf
(*) DNA as poly-ion in a nanopore: Smeets et al. "Salt dependence of ion transport and DNA translocation through solid-state nanopores" Nano Letters (2006) pdf
basic presentation of technique for forces on DNA in nanopores 1: Keyser et al. (*) "Direct force measurements on DNA in a solid-state nanopore" Nature Physics (2006) pdf
advanced text, forces on DNA in nanopores 2: van Dorp et al. "Origin of the electrophoretic force on DNA in solid-state nanopores" Nature Physics (2009) pdf
(*) hot topic, Nobel prize 2010 for graphene: Golovchenko et al. "Graphene as a subnanometre trans-electrode membrane" Nature (2010) pdf
resistance of pores: Hall "Resistance of a small circular pore" J. of General Physiology (1975) pdf
(*) Membranes and membrane proteins
membranes, good introduction from physical point of view: Heimburg "Thermal Biophysics of Membranes" chapter 1-3
(*)ATP motor is discussed in Question 13: Nelson "Biological Physics" chapter 11
(*)Review of E. coli flagellar motor: Berg "THE ROTARY MOTOR OF BACTERIAL FLAGELLA" Ann. Rev. Biochem. (2003) pdf
(*)Dependence on proton motive force: Berg et al. "The speed of the flagellar rotary motor of Escherichia coli varies linearly with protonmotive force" PNAS (2003) pdf
(*)Torque of the motor: Berg "TORQUE GENERATED BY THE FLAGELLAR MOTOR OF ESCHERICHIA-COLI" Biophys. J. (1993) pdf
"van der Waals" interactions
very good book: Parsegian, "Van der Waals forces" (as indicated in syllabus), Level 1 and Level 2
for van der Waals gas equation: e.g. Atkins et al., "Physical Chemistry", Molecular Interactions
nice review, calculation in class was taken from there: Holstein, "The van der Waals interaction", Am. J. Phys. 69 (2001) pdf
calculation for Q3 and more things: Hamaker, "The London - van der Waals Attraction", Physics IV (1937) pdf
background on DLVO: Parsegian, "Van der Waals forces", Level 1 and Level 2
the original book: Verwey and Overbeek "Theory of the stability of lyophobic colloids" 1948
screened Coulomb interaction for single colloids: Gutsche, Keyser, Kegler, Kremer, Linse, "Forces between single pairs of charged colloids in aqueous solutions" PRE 2007 pdf