TeachingMichaelmas 2010: Soft Matter and Biological PhysicsThe material is for your private use. Please do not distribute. PDFs of articles, where I have them, are accessible via links.Slides101008101011-13 and protein movie mpeg 101015 101018-20 101022 101025 101027-29 101101 101103 101105 101108 101110 101112 101115 101117 101119 101122 101124 101126 101129 101201 Question sheetsSheet 1Questions 1-5Paper for question 4 pdf Sheet 2Questions 6-10Sheet 3Questions 11-15Sheet 4A1-3Literature/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 from 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". Examinable topics are marked with (*). Read the paper 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" Proteins, folding and unfolding (*)Booksprotein 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 pdfforced 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 "van der Waals" interactions (*)Booksvery 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) pdfAtomic Force Microscopy (*)Reviewbackground 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 Optical Tweezers (*)Booksbackground 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 Reviewscomprehensive 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 Papersadvanced 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 DLVO 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 pdf(Colloid) Electrophoresis/Electroknietic phenomena (*)Reviewsconcise 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 linkDNA, 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 papersseminal paper: Wang et al. "Stretching DNA with Optical Tweezers", Biophysical Journal (1997) pdfseminal 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 Magnetic Tweezers and Super-coiled DNAResearch papersMagnetic tweezers, technique: Gosse and Croquette "Magnetic Tweezers: Micromanipulation and Force Measurements at the Molecular Level", Biophys. J. (2002) pdfpolymer dynamics: Crut et al. "Dynamics of phosphodiester synthesis by DNA ligase" PNAS (2008) 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 Entropic Trapping (*)Research 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) Electrophoresis (*)Booksgeneral 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 Nanopores (*)very biological perspective: Hille, "Ion Channels of Excitable Membranes", Chapter 11basic intro: Berg "Random walks in biology", chapter 1-4 Reviewsforces in nanopores 1: Keyser, van Dorp, Lemay, "Tether forces in DNA electrophoresis", Chem. Soc. Rev. (2010) pdfnice 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 1-3motor discussed in q14: Nelson "Biological Physics" chapter 11 |