TeachingMichaelmas 2011: Soft Matter and Biological PhysicsRay Goldstein and Ulrich KeyserRay's teaching page at DAMTP. 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 notesYou 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) .Slides 2011Slides: 111102 -- Other material: optical tweezers TETRIS -- MKS-CGS conversion from Parsegian bookSlides: 111104 Slides: 111109 Slides: 111111 Slides: 111114 -- Other material: protein movie mpeg Slides: 111121 Slides: 111123 -- Other material: shrinking nanopores avi Slides: 111130 -- Other material: swimming e.coli movies Berg Lab, Harvard one example avi and measuring torque with optical tweezers Question sheet(s) & Example classesPhysics example classesSmall 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 topicsBelow 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.General ideasfor 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 TweezersBooksbackground for Langevin equation and harmonic oscillators: Chaikin, Lubensky "Principles of Condensed Matter Physics" chapter 7.5more concise on Langevin and fluctuation dissipation: Dill, Bromber "Molecular Driving Forces" chapter 18 Reviews(*) comprehensive overview over most state of the art techniques: Neuman, Block, "Optical Trapping", Review of Scientific Instruments (2004) pdfvery 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 Research Papers(*) advanced paper: Bustamante et al. "Mechanical Processes in Biochemistry" (2004) pdflaser 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 LinksPadgett group in Glasgow has a lot of fun movies about optical tweezers linkMore 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 DNAResearch papers(*) 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, ...BooksDNA 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 ReviewsResearch papers(*) 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 MicroscopyReviewbackground on trapping on surfaces: Bustamante & Rivetti, "Visualizing protein-nucleic acid interactions on a large scale with the scanning force microscope" Ann. Rev. Biophy. (1996) pdfResearch Paperswritten by two main researchers in the field: Engel & Muller, "Observing single biomolecules at work with the atomic force microscope" Nature Structural Biology (2000) pdfseminal 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 unfoldingBooksprotein 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 Research Papersfolding 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 (Colloid) Electrophoresis/Electrokinetic phenomenaReviews(*) concise treatise of all major phenomena: Hunter et al., "Measurement and interpretation of electrokinetic phenomena", J. Coll. Interface Sci. (2007) pdfResearch paperstechnical development paper: Otto, et al. "Optical tweezers with 2.5 kHz bandwidth video detection for single-colloid electrophoresis" Rev. Sci. Instr. (2008) pdfpaper discussed in q7: Semenov, et al., "Single colloid electrophoresis" J. Coll. Interface Sci. (2009) pdf LinksSantiago Lab at Stanford for imaging of flows in channels link(*) Entropic TrappingResearch papersnanotechnology: Turner, Cabodi, Craighead "Confinement-Induced Entropic Recoil of Single DNA Molecules in a Nanofluidic Structure" Phys. Rev. Lett. (2002) pdfin gels: Liu, Li, Asher "Entropic trapping of macromolecules by mesoscopic periodic voids in a polymer hydrogel" Nature (1999) pdf (Gel) ElectrophoresisBooksgeneral polymer physics and dynamics: Rubinstein "Polymer Physics", chapters 7-9for reptation and relaxation times: Strobl "The Physics of Polymers", Chapter 3,8 Reviewsmodern perspective - practical, nice: Viovy, "Electrophoresis of DNA and other polyelectrolytes: Physical mechanisms", Rev. Mod. Phys. (2000) pdfbasic ideas, solution for q11: Zimm and Levene, "Problems and prospects in the theory of gel electrophoresis of DNA" Qart. Rev. Biophys (1992) pdf (*) Nanoporesvery biological perspective: Hille, "Ion Channels of Excitable Membranes", Chapter 11basic intro: Berg "Random walks in biology", chapter 1-4 Reviews(*) 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 Research papersseminal paper: Kasianowicz et al. "Characterization of individual polynucleotide molecules using a membrane channel" pdfadvanced 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 proteinsBooksmembranes, 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 Reviews(*)Review of E. coli flagellar motor: Berg "THE ROTARY MOTOR OF BACTERIAL FLAGELLA" Ann. Rev. Biochem. (2003) pdfResearch Papers(*)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" interactionsBooksvery good book: Parsegian, "Van der Waals forces" (as indicated in syllabus), Level 1 and Level 2for van der Waals gas equation: e.g. Atkins et al., "Physical Chemistry", Molecular Interactions Reviewsnice review, calculation in class was taken from there: Holstein, "The van der Waals interaction", Am. J. Phys. 69 (2001) pdfResearch Paperscalculation for Q3 and more things: Hamaker, "The London - van der Waals Attraction", Physics IV (1937) pdfDLVO theoryBooksbackground on DLVO: Parsegian, "Van der Waals forces", Level 1 and Level 2the original book: Verwey and Overbeek "Theory of the stability of lyophobic colloids" 1948 ReviewsResearch Papersscreened Coulomb interaction for single colloids: Gutsche, Keyser, Kegler, Kremer, Linse, "Forces between single pairs of charged colloids in aqueous solutions" PRE 2007 pdfSlides from 2010101008 101011-13 and protein movie mpeg 101015 101018-20 101022 101025 101027-29 101101 101103 101105 101108101110 101112 101115 101117 101119 101122 101124 101126 101129 101201 |