APPLIED BIOPHYSICS

By W. DANAI

CONTENTS THE BUILDING BLOCKS PROTEINS LIPIDS NUCLEIC ACIDS CARBOHYDRATES WATER PROTEOGLYCANS AND GLYCOPROTEINS CELLS (COMPLEX CONSTRUCTS OF BIOMOLECULES) VIRUSES (COMPLEX CONSTRUCTS OF BIOMOLECULES) BACTERIA (COMPLEX CONSTRUCTS OF BIOMOLECULES) 1 10 OTHER MOLECULES FURTHER READING TUTORIAL QUESTIONS MESOSCOPIC FORCES COHESIVE FORCES HYDROGEN BONDING ELECTROSTATICS UNSCREENED ELECTROSTATIC INTERACTIONS SCREENED ELECTROSTATIC INTERACTIONS THE FORCE BETWEEN CHARGED SPHERES IN SOLUTION STERIC AND FLUCTUATION FORCES DEPLETION FORCES HYDRODYNAMIC INTERACTIONS DIRECT EXPERIMENTAL MEASUREMENTS OF INTERMOLECULAR AND SURFACE FORCES PHASE TRANSITIONS THE BASICS HELIX–COIL TRANSITION GLOBULE–COIL TRANSITION CRYSTALLISATION LIQUID–LIQUID DEMIXING (PHASE SEPARATION) LIQUID CRYSTALLINITY LIQUID–NEMATIC–SMECTIC TRANSITIONS DEFECTS MORE EXOTIC POSSIBILITIES FOR LIQUID CRYSTALLINE PHASES MOTILITY DIFFUSION LOW REYNOLD’S NUMBER DYNAMICS FIRST PASSAGE PROBLEM RATE THEORIES OF CHEMICAL REACTIONS AGGREGATING SELF-ASSEMBLY SURFACTANTS VIRUSES SELF-ASSEMBLY OF PROTEINS POLYMERISATION OF CYTOSKELETAL FILAMENTS (MOTILITY) SURFACE PHENOMENA SURFACE TENSION ADHESION WETTING CAPILLARITY EXPERIMENTAL TECHNIQUES FRICTION OTHER SURFACE PHENOMENA TUTORIAL QUESTION BIOMACROMOLECULES FLEXIBILITY OF MACROMOLECULES GOOD/BAD SOLVENTS AND THE SIZE OF POLYMERS ELASTICITY DAMPED MOTION OF SOFT MOLECULES DYNAMICS OF POLYMER CHAINS TOPOLOGY OF POLYMER CHAINS – SUPER COILING CHARGED IONS AND POLYMERS DEBYE–HUCKEL THEORY IONIC RADIUS THE BEHAVIOUR OF POLYELECTROLYTES DONNAN EQUILIBRIA TITRATION CURVES POISSON–BOLTZMANN THEORY FOR CYLINDRICAL CHARGE DISTRIBUTIONS CHARGE CONDENSATION OTHER POLYELECTROLYTE PHENOMENA 10 MEMBRANES 10 1 UNDULATIONS 10 2 BENDING RESISTANCE 10 3 ELASTICITY 10 4 INTERMEMBRANE FORCES 11 CONTINUUM MECHANICS 11 1 STRUCTURAL MECHANICS 11 2 COMPOSITES 11 3 FOAMS 11 4 FRACTURE 11 5 MORPHOLOGY 12 BIORHEOLOGY 12 1 STORAGE AND LOSS MODULI 12 2 RHEOLOGICAL FUNCTIONS 12 3 EXAMPLES FROM BIOLOGY NEUTRAL POLYMER SOLUTIONS POLYELECTROLYTES GELS COLLOIDS LIQUID CRYSTALLINE POLYMERS GLASSY MATERIALS MICRO?UIDICS IN CHANNELS 13 EXPERIMENTAL TECHNIQUES 13 1 STATIC SCATTERING TECHNIQUES 13 2 DYNAMIC SCATTERING TECHNIQUES 13 3 OSMOTIC PRESSURE 13 4 FORCE MEASUREMENT 13 5 ELECTROPHORESIS 13 6 SEDIMENTATION 13 7 RHEOLOGY 13 8 TRIBOLOGY 13 9 SOLID PROPERTIES 14 MOTORS 14 1 SELF-ASSEMBLING MOTILITY – POLYMERISATION OF ACTIN AND TUBULIN 14 2 PARALLELISED LINEAR STEPPER MOTORS – STRIATED MUSCLE 14 3 ROTATORY MOTORS 14 4 RATCHET MODELS 14 5 OTHER SYSTEMS 15 STRUCTURAL BIOMATERIALS 15 1 CARTILAGE – TOUGH SHOCK ABSORBER IN HUMAN JOINTS 15 2 SPIDER SILK 15 3 ELASTIN AND RESILIN 15 4 BONE 15 5 ADHESIVE PROTEINS 15 6 NACRE AND MINERAL COMPOSITES 16 PHASE BEHAVIOUR OF DNA 16 1 CHROMATIN – NATURALLY PACKAGED DNA CHAINS 16 2 DNA COMPACTION – AN EXAMPLE OF POLYELECTROLYTE COMPLEXATION 16 3 FACILITATED DIFFUSION