Atomic Force Microscopy in Liquid -- Contents -- Preface -- List of Contributors -- Part I General Atomic Force Microscopy -- 1 AFM: Basic Concepts -- 1.1 Atomic Force Microscope: Principles -- 1.2 Piezoelectric Scanners -- 1.2.1 Piezoelectric Scanners for Imaging in Liquids -- 1.3 Tips and Cantilevers -- 1.3.1 Cantilever Calibration -- 1.3.2 Tips and Cantilevers for Imaging in Liquids -- 1.3.3 Cantilever Dynamics in Liquids -- 1.4 Force Detection Methods for Imaging in Liquids -- 1.4.1 Piezoelectric Cantilevers and Tuning Forks -- 1.4.2 Laser Beam Deflection Method -- 1.4.2.1 Liquid Cells and Beam Deflection -- 1.5 AFM Operation Modes: Contact, Jumping/Pulsed, Dynamic -- 1.5.1 Contact Mode -- 1.5.2 Jumping and Pulsed Force Mode -- 1.5.3 Dynamic Modes -- 1.5.3.1 Liquid Cells and Dynamic Modes -- 1.6 The Feedback Loop -- 1.7 Image Representation -- 1.8 Artifacts and Resolution Limits -- 1.8.1 Artifacts Related to the Geometry of the Tip -- 1.8.2 Artifacts Related to the Feedback Loop -- 1.8.3 Resolution Limits -- Acknowledgments -- References -- 2 Carbon Nanotube Tips in Atomic Force Microscopy with Applications to Imaging in Liquid -- 2.1 Introduction -- 2.2 Fabrication of CNT AFM Probes -- 2.2.1 Mechanical Attachment -- 2.2.2 CNT Attachment Techniques Employing Magnetic and Electric Fields -- 2.2.3 Direct Growth of CNT Tips -- 2.2.4 Emerging CNT Attachment Techniques -- 2.2.5 Postfabrication Modification of the CNT Tip -- 2.2.5.1 Shortening -- 2.2.5.2 Coating with Metal -- 2.3 Chemical Functionalization -- 2.3.1 Functionalization of the CNT Free End -- 2.3.2 Coating the CNT Sidewall -- 2.4 Mechanical Properties of CNTs in Relation to AFM Applications -- 2.4.1 CNT Atomic Structure -- 2.4.2 Mechanical Properties of CNT AFM Tips -- 2.5 Dynamics of CNT Tips in Liquid -- 2.5.1 Interaction of Microfabricated AFM Tips and Cantilevers in Liquid.

2.5.2 CNT AFM Tips in Liquid -- 2.5.3 Interaction of CNT with Liquids -- 2.5.3.1 CNT Tips at the Air-Liquid Interface During Approach -- 2.5.3.2 CNT Tips at the Liquid-Solid Interface -- 2.5.3.3 CNT Tips at the Air-Liquid Interface during Withdrawal -- 2.6 Performance and Resolution of CNT Tips in Liquid -- 2.6.1 Performance of CNT AFM Tips When Imaging in Liquid -- 2.6.2 Biological Imaging in Liquid Medium with CNT AFM Tips -- 2.6.3 Cell Membrane Penetration and Applications of Intracellular CNT AFM Probes -- References -- 3 Force Spectroscopy -- 3.1 Introduction -- 3.2 Measurement of Force Curves -- 3.2.1 Analysis of Force Curves Taken in Air -- 3.2.2 Analysis of Force Curves in a Liquid -- 3.3 Measuring Surface Forces by the Surface Force Apparatus -- 3.4 Forces between Macroscopic Bodies -- 3.5 Theory of DLVO Forces between Two Surfaces -- 3.6 Van der Waals Forces - the Hamaker Constant -- 3.7 Electrostatic Force between Surfaces in a Liquid -- 3.8 Spatially Resolved Force Spectroscopy -- 3.9 Force Spectroscopy Imaging of Single DNA Molecules -- 3.10 Solvation Forces -- 3.11 Hydrophobic Forces -- 3.12 Steric Forces -- 3.13 Conclusive Remarks -- Acknowledgments -- References -- 4 Dynamic-Mode AFM in Liquid -- 4.1 Introduction -- 4.2 Operation Principles -- 4.2.1 Amplitude and Phase Modulation AFM (AM- and PM-AFM) -- 4.2.2 Frequency-Modulation AFM (FM-AFM) -- 4.3 Instrumentation -- 4.3.1 Cantilever Excitation -- 4.3.2 Cantilever Deflection Measurement -- 4.3.3 Operating Conditions -- 4.3.4 AM-AFM -- 4.3.4.1 FM-AFM -- 4.3.4.2 PM-AFM -- 4.4 Quantitative Force Measurements -- 4.4.1 Calibration of Spring Constant -- 4.4.2 Conservative and dissipative forces -- 4.4.3 Solvation Force Measurements -- 4.4.3.1 Inorganic Solids in Nonpolar Liquids -- 4.4.3.2 Measurements in Pure Water -- 4.4.3.3 Solvation Forces in Biological Systems.

4.4.4 Single-Molecule Force Spectroscopy -- 4.4.4.1 Unfolding and ''Stretching'' of Biomolecules -- 4.4.4.2 Ligand-Receptor Interactions -- 4.5 High-Resolution Imaging -- 4.5.1 Solid Crystals -- 4.5.2 Biomolecular Assemblies -- 4.5.3 Water Distribution -- 4.6 Summary and Future Prospects -- References -- 5 Fundamentals of AFM Cantilever Dynamics in Liquid Environments -- 5.1 Introduction -- 5.2 Review of Fundamentals of Cantilever Oscillation -- 5.3 Hydrodynamics of Cantilevers in Liquids -- 5.4 Methods of Dynamic Excitation -- 5.4.1 Review of Cantilever Excitation Methods -- 5.4.2 Theory -- 5.4.2.1 Direct Forcing -- 5.4.2.2 Ideal Piezo/Acoustic -- 5.4.2.3 Thermal -- 5.4.2.4 Comparison of Excitation Methods -- 5.4.3 Practical Considerations for Acoustic Method -- 5.4.4 Photothermal Method -- 5.4.5 Frequency Modulation Considerations in Liquids -- 5.5 Dynamics of Cantilevers Interacting with Samples in Liquids -- 5.5.1 Experimental Observations of Oscillating Probes Interacting with Samples in Liquids -- 5.5.2 Modeling and Numerical Simulations of Oscillating Probes Interacting with Samples in Liquids -- 5.5.3 Compositional Mapping in Liquids -- 5.5.4 Implications for Force Spectroscopy in Liquids -- 5.6 Outlook -- References -- 6 Single-Molecule Force Spectroscopy -- 6.1 Introduction -- 6.1.1 Why Single-Molecule Force Spectroscopy? -- 6.1.2 SMFS in Biology -- 6.1.3 SMFS Techniques and Ranges -- 6.2 AFM-SMFS Principles -- 6.2.1 Length-Clamp Mode -- 6.2.2 Force-Clamp Mode -- 6.3 Dynamics of Adhesion Bonds -- 6.3.1 Bond Dissociation Dynamics in Length Clamp -- 6.3.2 General Considerations -- 6.3.3 Bond Dissociation Dynamics in Force Clamp -- 6.3.3.1 The Need for Robust Statistics -- 6.4 Specific versus Other Interactions -- 6.4.1 Intramolecular Single-Molecule Markers -- 6.4.1.1 The Wormlike Chain: an Elasticity Model -- 6.4.1.2 Proteins.

6.4.1.3 DNA and Polysaccharides -- 6.4.2 Intermolecular Single-Molecule Markers -- 6.5 Steered Molecular Dynamics Simulations -- 6.6 Biological Findings Using AFM-SMFS -- 6.6.1 Titin as an Adjustable Molecular Spring in the Muscle Sarcomere -- 6.6.2 Monitoring the Folding Process by Force-Clamp Spectroscopy -- 6.6.3 Intermolecular Binding Forces and Energies in Pairs of Biomolecules -- 6.6.4 New Insights in Catalysis Revealed at the Single-Molecule Level -- 6.7 Concluding Remarks -- Acknowledgments -- Disclaimer -- References -- 7 High-Speed AFM for Observing Dynamic Processes in Liquid -- 7.1 Introduction -- 7.2 Theoretical Derivation of Imaging Rate and Feedback Bandwidth -- 7.2.1 Imaging Time and Feedback Bandwidth -- 7.2.2 Time Delays -- 7.3 Techniques Realizing High-Speed Bio-AFM -- 7.3.1 Small Cantilevers -- 7.3.2 Fast Amplitude Detector -- 7.3.3 High-Speed Scanner -- 7.3.4 Active Damping Techniques -- 7.3.5 Suppression of Parachuting -- 7.3.6 Fast Phase Detector -- 7.4 Substrate Surfaces -- 7.4.1 Supported Planar Lipid Bilayers -- 7.4.1.1 Choice of Alkyl Chains -- 7.4.1.2 Choice of Head Groups -- 7.4.2 Streptavidin 2D Crystal Surface -- 7.5 Imaging of Dynamic Molecular Processes -- 7.5.1 Bacteriorhodopsin Crystal Edge -- 7.5.2 Photoactivation of Bacteriorhodopsin -- 7.6 Future Prospects of High-Speed AFM -- 7.6.1 Imaging Rate and Low Invasiveness -- 7.6.2 High-Speed AFM Combined with Fluorescence Microscope -- 7.7 Conclusion -- References -- 8 Integration of AFM with Optical Microscopy Techniques -- 8.1 Introduction -- 8.1.1 Combining AFM with Fluorescence Microscopy -- 8.1.1.1 Epifluorescence Microscopy -- 8.1.2 Examples of Applications -- 8.1.2.1 Ca2+ Fluorescence Microscopy -- 8.1.2.2 AFM - Epifluorescence Microscopy -- 8.2 Combining AFM with IRM and TIRF microscopy -- 8.2.1 Interference Reflection Microscopy -- 8.2.1.1 Optical Setup.

8.2.2 Total Internal Reflection Fluorescence Microscopy -- 8.2.2.1 Optical Setup -- 8.2.2.2 Applications of Combined AFM-TIRF and AFM-IRM Microscopy -- 8.3 Combining AFM and FRET -- 8.3.1 FRET -- 8.3.2 FRET and Near-Field Scanning Optical Microscopy (NSOM) -- 8.4 FRET-AFM -- 8.5 Sample Preparation and Experiment Setup -- 8.5.1 Cell Culture, Transfection, and Fura-Loading -- 8.5.2 Cantilever Preparation -- 8.5.3 Typical Experimental Procedure -- References -- Part II Biological Applications -- 9 AFM Imaging in Liquid of DNA and Protein-DNA Complexes -- 9.1 Overview: the Study of DNA at Nanoscale Resolution -- 9.2 Sample Preparation for AFM Imaging of DNA and Protein-DNA Complexes -- 9.3 AFM of DNA in Aqueous Solutions -- 9.3.1 Elevated Resolution in Aqueous Solutions -- 9.3.2 Segmental Mobility of DNA -- 9.4 AFM Imaging of Alternative DNA Conformations -- 9.4.1 Cruciforms in DNA -- 9.4.2 Intramolecular Triple Helices -- 9.4.3 Four-Way DNA Junctions and DNA Recombination -- 9.5 Dynamics of Protein-DNA Interactions -- 9.5.1 Site-Specific Protein-DNA Complexes -- 9.5.2 Chromatin Dynamics Time-Lapse AFM -- 9.6 DNA Condensation -- 9.7 Conclusions -- Acknowledgments -- References -- 10 Stability of Lipid Bilayers as Model Membranes: Atomic Force Microscopy and Spectroscopy Approach -- 10.1 Biological Membranes -- 10.1.1 Cell Membrane -- 10.1.2 Supported Lipid Bilayers -- 10.2 Mechanical Characterization of Lipid Membranes -- 10.2.1 Breakthrough Force as a Molecular Fingerprint -- 10.2.2 AFM Tip-Lipid Bilayer Interaction -- 10.2.3 Effect of Chemical Composition on the Mechanical Stability of Lipid Bilayers -- 10.2.4 Effect of Ionic Strength on the Mechanical Stability of Lipid Bilayers -- 10.2.5 Effect of Different Cations on the Mechanical Stability of Lipid Bilayers -- 10.2.6 Effect of Temperature on the Mechanical Stability of Lipid Bilayers.

10.2.7 The Case of Phase-Segregated Lipid Bilayers.