CONTENTS -- Acknowledgements -- CHAPTER 1 AN INTRODUCTION -- CHAPTER 2 APPARATUS -- 2.1. The atomic force microscope -- 2.2. Piezoelectric scanners -- 2.3. Probes and cantilevers -- 2.3.1. Cantilever geometry -- 2.3.2. Tip shape -- 2.3.3. Tip functionality -- 2.4. Sample holders -- 2.4.1. Liquid cells -- 2.5. Detection methods -- 2.5.1. Optical detectors: laser beam deflection -- 2.5.2. Optical detectors: interferometry -- 2.5.3. Electrical detectors: electron tunnelling -- 2.5.4. Electrical detectors: capacitance -- 2.5.5. Electrical detectors: piezoelectric cantilevers -- 2.6. Control systems -- 2.6.1. AFM electronics -- 2.6.2. Operation of the electronics -- 2.6.3. Feedback control loops -- 2.6.4. Design limitations -- 2.6.5. Enhancing the performance of large scanners -- 2.7. Vibration isolation: thermal and mechanical -- 2.8. Calibration -- 2.8.1. Piezoelectric scanner non-linearity -- 2.8.2. Tip related factors: convolution -- 2.8.3. Calibration standards -- 2.8.4. Tips for scanning a calibration specimen -- 2.9. Integrated AFMs -- 2.9.1. Combined AFM-light microscope (AFM-LM) -- 2.9.2. 'Submarine' AFM - the combined AFM - Langmuir Trough -- 2.9.3. Combined AFM-surface plasmon resonance (AFM-SPR) -- 2.9.4. Cryo-AFM -- References -- Useful information sources -- CHAPTER 3 BASIC PRINCIPLES -- 3.1. Forces -- 3.1.1. The Van der Waals force and force-distance curves -- 3.1.2. The electrostatic force -- 3.1.3. Capillary and adhesive forces -- 3.1.4. Double layer forces -- 3.2. Imaging modes -- 3.2.1. Contact dc mode -- 3.2.2. Ac modes: Tapping and non-contact -- Tapping in air -- Tapping under liquid -- True, non-contact ac mode -- Tuning the cantilever -- Influence of drive frequency -- 3.2.3. Deflection mode -- 3.3. Image types -- 3.3.1. Topography -- 3.3.2. Frictional force -- 3.3.3. Phase -- 3.4. Substrates -- 3.4.1. Mica -- 3.4.2. Glass.

3.4.3. Graphite -- 3.5. Common problems -- 3.5.1. Thermal drift -- 3.5.2. Multiple tip effects -- 3.5.3. The 'pool' artifact -- 3.5.4. Optical interference on highly reflective samples -- 3.5.5. Sample roughness -- 3.5.6. Sample mobility -- 3.5.7. Imaging under liquid -- 3.6. Getting started -- 3.6.1. DNA -- 3.6.2. Troublesome large samples -- 3.7. Image optimisation -- 3.7.1. Grey levels and colour tables -- 3.7.2. Brightness and contrast -- 3.7.3. High and low pass filtering -- 3.7.4. Normalisation and plane fitting -- 3.7.5. Despike -- 3.7.6. Fourier filtering -- 3.7.7. Correlation averaging -- 3.7.8. Stereographs and anaglyphs -- 3.7.9. Do your homework! -- References -- CHAPTER 4 MACROMOLECULES -- 4.1. Imaging methods -- 4.1.1. Tip adhesion, molecular damage and displacement -- 4.1.2. Depositing macromolecules onto substrates -- 4.1.3. Metal coated samples -- 4.1.4. Imaging in air -- 4.1.5. Imaging under non-aqueous liquids -- 4.1.6. Binding molecules to the substrate -- 4.1.7. Imaging under water or buffers -- 4.2. Nucleic acids: DNA -- 4.2.1. Imaging DNA -- 4.2.2. DNA conformation, size and shape -- 4.2.3. DNA-protein interactions -- 4.2.4. Location and mapping of specific sites -- 4.2.5. Chromosomes -- 4.3. Nucleic acids: RNA -- 4.4. Polysaccharides -- 4.4.1. Imaging polysaccharides -- 4.4.2. Size, shape, structure and conformation -- 4.4.3. Aggregates, networks and gels -- 4.4.4. Cellulose, plant cell walls and starch -- 4.4.5. Proteoglycans and mucins -- 4.5. Proteins -- 4.5.1. Globular proteins -- 4.5.2. Antibodies -- 4.5.3. Fibrous proteins -- References: Selected Books and Reviews -- Selected Research Papers -- CHAPTER 5 INTERFACIAL SYSTEMS -- 5.1. Introduction to interfaces -- 5.1.1. Surface activity -- 5.1.2. AFM of interfacial systems -- 5.1.3. The Langmuir trough -- 5.1.4. Langmuir-Blodgett film transfer -- 5.2. Sample preparation.

5.2.1. Cleaning protocols: glassware and trough -- 5.2.2. Substrates -- 5.2.3. Performing the dip -- 5.3. Phospholipids -- 5.3.1. Early AFM studies of phospholipid films -- 5.3.2. Modification of phospholipid bilayers with the AFM -- 5.3.3. Studying intrinsic bilayer properties by AFM -- 5.3.4. Ripple phases in phospholipid bilayers -- 5.3.5. Mixed phospholipid films -- 5.3.6. Effect of supporting layers -- 5.3.7. Dynamic processes of phopholipid layers -- 5.4. Liposomes and intact vesicles -- 5.5. Lipid-protein mixed films -- 5.5.1. High resolution studies of phospholipid bilayers -- 5.6. Miscellaneous lipid films/surfactant films -- 5.7. Interfacial protein films -- 5.7.1. Specific precautions -- 5.7.2. AFM studies of interfacial protein films -- References -- CHAPTER 6 ORDERED MACROMOLECULES -- 6.1. Three-dimensional crystals -- 6.1.1. Crystalline cellulose -- 6.1.2. Protein crystals -- 6.1.3. Nucleic acid crystals -- 6.1.4. Viruses and virus crystals -- 6.2. Two dimensional protein crystals: an introduction -- 6.2.1. What does AFM have to offer? -- 6.2.2. Sample preparation: membrane proteins -- 6.2.3. Sample preparation: soluble proteins -- 6.3. AFM studies of 2D membrane protein crystals -- 6.3.1. Purple membrane (bacteriorhodopsin) -- 6.3.2. Gap junctions -- 6.3.3. Photosynthetic protein membranes -- 6.3.4. ATPase in kidney membranes -- 6.3.5. OmpFporin -- 6.3.6. Bacterial Slayers -- 6.3.7. Bacteriophage 29 head-tail connector -- 6.3.8. AFM imaging of membrane dynamics -- 6.3.9. Force spectroscopy of membrane proteins -- 6.3.10. Gas vesicle protein -- 6.4. AFM studies of 2D crystals of soluble proteins -- 6.4.1. Imaging conditions -- 6.4.2. Electrostatic considerations -- References -- CHAPTER 7 CELLS, TISSUE AND BIOMINERALS -- 7.1. Imaging methods -- 7.1.1. Sample preparation -- 7.1.2. Force mapping and mechanical measurements.

7.2. Microbial cells: bacteria, spores and yeasts -- 7.2.1. Bacteria -- 7.2.2. Yeasts -- 7.3. Blood cells -- 7.3.1. Erythrocytes -- 7.3.2. Leukocytes and lymphocytes -- 7.3.3. Platelets -- 7.4. Neurons and Glial cells -- 7.5. Epithelial cells -- 7.6. Non-confluent renal cells -- 7.7. Endothelial cells -- 7.8. Cardiocytes -- 7.9. Other mammalian cells -- 7.10. Plant cells -- 7.11. Tissue -- 7.11.1. Embedded sections -- 7.11.2. Embedment-free sections -- 7.11.3. Hydrated sections -- 7.11.4. Freeze-fracture replicas -- 7.11.5. Immunolabelling -- 7.12. Biominerals -- 7.12.1. Bone, tendon and cartilage -- 7.12.2. Teeth -- 7.12.3. Shells -- References: selected reviews -- Selected references -- CHAPTER 8 OTHER PROBE MICROSCOPES -- 8.1. Overview -- 8.2. Scanning tunnelling microscope (STM) -- 8.3. Scanning near-field optical microscope (SNOM) -- 8.4. Scanning ion conductance microscope (SICM) -- 8.5. Scanning thermal microscope (SThM) -- 8.6. Optical tweezers and the photonic force microscope (PPM) -- References -- CHAPTER 9 FORCE SPECTROSCOPY -- 9.1. Force measurement with the AFM -- 9.2. First steps in force spectroscopy: from raw data to force-distance curves -- 9.2.1. Quantifying cantilever displacement -- 9.2.2. Determining cantilever spring constants -- 9.2.3. Anatomy of a force-distance curve -- 9.3. Pulling methods -- 9.3.1. Intrinsic elastic properties of molecules -- 9.3.2. Molecular recognition force spectroscopy -- 9.3.3. Chemical force microscopy (CPM) -- 9.4. Pushing methods -- 9.4.1. Colloidal probe microscopy (CPM) -- 9.4.2. How to make a colloid probe cantilever assembly -- 9.4.3. Deformation and indentation methods -- 9.5. Analysis of force-distance curves -- 9.5.1. Worm-like chain and freely jointed chain models -- 9.5.2. Molecular interactions -- 9.5.3. Deformation analysis -- 9.5.4. Adhesive force at pull-off.

9.5.5. Elastic indentation depth, , and contact radius, a, during deformation -- 9.5.6. Contact radius at zero load -- 9.5.7. Colloidal forces -- References -- SPM Books -- Index.