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Atomic Force Microscopy in Liquid: Biological Applications [Kõva köide]

Edited by (Purdue University, West Lafayette, USA), Edited by (CSIC, Madrid, Spain)
  • Formaat: Hardback, 402 pages, kõrgus x laius x paksus: 246x173x23 mm, kaal: 816 g
  • Ilmumisaeg: 04-Apr-2012
  • Kirjastus: Blackwell Verlag GmbH
  • ISBN-10: 3527327584
  • ISBN-13: 9783527327584
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Atomic Force Microscopy in Liquid: Biological ApplicationsSuurem pilt
  • Formaat: Hardback, 402 pages, kõrgus x laius x paksus: 246x173x23 mm, kaal: 816 g
  • Ilmumisaeg: 04-Apr-2012
  • Kirjastus: Blackwell Verlag GmbH
  • ISBN-10: 3527327584
  • ISBN-13: 9783527327584
Teised raamatud teemal:
Püsilink: https://www.kriso.ee/db/9783527327584.html
This first book to focus on all principles and aspects of AFM in liquid phase is perfectly structured, making it easy-to-follow for non-AFM specialists. At the same time, it is an excellent introduction for researchers wishing to use this important technique for evaluating biological material and biological applications.

About 40 % of current atomic force microscopy (AFM) research is performed in liquids, making liquid-based AFM a rapidly growing and
important tool for the study of biological materials. This book focuses on the underlying principles and experimental aspects of AFM under
liquid, with an easy-to-follow organization intended for new AFM scientists. The book also serves as an up-to-date review of new AFM techniques developed especially for biological samples.
Aimed at physicists, materials scientists, biologists, analytical chemists, and medicinal chemists. An ideal reference book for libraries.

From the contents:

Part I: General Atomic Force Microscopy
* AFM: Basic Concepts
* Carbon Nanotube Tips in Atomic Force Microscopy with
* Applications to Imaging in Liquid
* Force Spectroscopy
* Atomic Force Microscopy in Liquid
* Fundamentals of AFM Cantilever Dynamics in Liquid
* Environments
* Single-Molecule Force Spectroscopy
* High-Speed AFM for Observing Dynamic Processes in Liquid
* Integration of AFM with Optical Microscopy Techniques

Part II: Biological Applications
* DNA and Protein-DNA Complexes
* Single-Molecule Force Microscopy of Cellular Sensors
* AFM-Based Single-Cell Force Spectroscopy
* Nano-Surgical Manipulation of Living Cells with the AFM
Preface xiii
List of Contributors
xv
Part I General Atomic Force Microscopy
1(230)
1 AFM: Basic Concepts
3(32)
Fernando Moreno-Herrero
Julio Gomez-Herrero
1.1 Atomic Force Microscope: Principles
3(2)
1.2 Piezoelectric Scanners
5(3)
1.2.1 Piezoelectric Scanners for Imaging in Liquids
8(1)
1.3 Tips and Cantilevers
8(7)
1.3.1 Cantilever Calibration
10(1)
1.3.2 Tips and Cantilevers for Imaging in Liquids
11(2)
1.3.3 Cantilever Dynamics in Liquids
13(2)
1.4 Force Detection Methods for Imaging in Liquids
15(4)
1.4.1 Piezoelectric Cantilevers and Tuning Forks
15(2)
1.4.2 Laser Beam Deflection Method
17(1)
1.4.2.1 Liquid Cells and Beam Deflection
18(1)
1.5 AFM Operation Modes: Contact, Jumping/Pulsed, Dynamic
19(5)
1.5.1 Contact Mode
19(1)
1.5.2 Jumping and Pulsed Force Mode
20(2)
1.5.3 Dynamic Modes
22(1)
1.5.3.1 Liquid Cells and Dynamic Modes
23(1)
1.6 The Feedback Loop
24(1)
1.7 Image Representation
25(3)
1.8 Artifacts and Resolution Limits
28(7)
1.8.1 Artifacts Related to the Geometry of the Tip
28(2)
1.8.2 Artifacts Related to the Feedback Loop
30(1)
1.8.3 Resolution Limits
31(1)
Acknowledgments
32(1)
References
32(3)
2 Carbon Nanotube Tips in Atomic Force Microscopy with Applications to Imaging in Liquid
35(30)
Edward D. de Asis, Jr.
Joseph Leung
Cattien V. Nguyen
2.1 Introduction
35(2)
2.2 Fabrication of CNT AFM Probes
37(7)
2.2.1 Mechanical Attachment
38(1)
2.2.2 CNT Attachment Techniques Employing Magnetic and Electric Fields
39(2)
2.2.3 Direct Growth of CNT Tips
41(2)
2.2.4 Emerging CNT Attachment Techniques
43(1)
2.2.5 Postfabrication Modification of the CNT Tip
43(1)
2.2.5.1 Shortening
43(1)
2.2.5.2 Coating with Metal
44(1)
2.3 Chemical Functionalization
44(2)
2.3.1 Functionalization of the CNT Free End
45(1)
2.3.2 Coating the CNT Sidewall
45(1)
2.4 Mechanical Properties of CNTs in Relation to AFM Applications
46(4)
2.4.1 CNT Atomic Structure
47(2)
2.4.2 Mechanical Properties of CNT AFM Tips
49(1)
2.5 Dynamics of CNT Tips in Liquid
50(8)
2.5.1 Interaction of Microfabricated AFM Tips and Cantilevers in Liquid
50(2)
2.5.2 CNT AFM Tips in Liquid
52(1)
2.5.3 Interaction of CNT with Liquids
52(2)
2.5.3.1 CNT Tips at the Air-Liquid Interface During Approach
54(2)
2.5.3.2 CNT Tips at the Liquid-Solid Interface
56(2)
2.5.3.3 CNT Tips at the Air-Liquid Interface during Withdrawal
58(1)
2.6 Performance and Resolution of CNT Tips in Liquid
58(7)
2.6.1 Performance of CNT AFM Tips When Imaging in Liquid
58(1)
2.6.2 Biological Imaging in Liquid Medium with CNT AFM Tips
59(1)
2.6.3 Cell Membrane Penetration and Applications of Intracellular CNT AFM Probes
60(1)
References
61(4)
3 Force Spectroscopy
65(22)
Arturo M. Baro
3.1 Introduction
65(2)
3.2 Measurement of Force Curves
67(3)
3.2.1 Analysis of Force Curves Taken in Air
68(2)
3.2.2 Analysis of Force Curves in a Liquid
70(1)
3.3 Measuring Surface Forces by the Surface Force Apparatus
70(1)
3.4 Forces between Macroscopic Bodies
71(1)
3.5 Theory of DLVO Forces between Two Surfaces
71(1)
3.6 Van der Waals Forces - the Hamaker Constant
72(1)
3.7 Electrostatic Force between Surfaces in a Liquid
72(4)
3.8 Spatially Resolved Force Spectroscopy
76(2)
3.9 Force Spectroscopy Imaging of Single DNA Molecules
78(1)
3.10 Solvation Forces
79(2)
3.11 Hydrophobic Forces
81(1)
3.12 Steric Forces
81(2)
3.13 Conclusive Remarks
83(4)
Acknowledgments
83(1)
References
83(4)
4 Dynamic-Mode AFM in Liquid
87(34)
Takeshi Fukuma
Michael J. Higgins
4.1 Introduction
87(1)
4.2 Operation Principles
88(2)
4.2.1 Amplitude and Phase Modulation AFM (AM- and PM-AFM)
88(1)
4.2.2 Frequency-Modulation AFM (FM-AFM)
89(1)
4.3 Instrumentation
90(7)
4.3.1 Cantilever Excitation
90(1)
4.3.2 Cantilever Deflection Measurement
91(2)
4.3.3 Operating Conditions
93(1)
4.3.4 AM-AFM
93(2)
4.3.4.1 FM-AFM
95(1)
4.3.4.2 PM-AFM
96(1)
4.4 Quantitative Force Measurements
97(13)
4.4.1 Calibration of Spring Constant
98(3)
4.4.2 Conservative and dissipative forces
101(2)
4.4.3 Solvation Force Measurements
103(1)
4.4.3.1 Inorganic Solids in Nonpolar Liquids
104(2)
4.4.3.2 Measurements in Pure Water
106(1)
4.4.3.3 Solvation Forces in Biological Systems
106(2)
4.4.4 Single-Molecule Force Spectroscopy
108(1)
4.4.4.1 Unfolding and "Stretching" of Biomolecules
108(2)
4.4.4.2 Ligand-Receptor Interactions
110(1)
4.5 High-Resolution Imaging
110(6)
4.5.1 Solid Crystals
112(1)
4.5.2 Biomolecular Assemblies
113(1)
4.5.3 Water Distribution
114(2)
4.6 Summary and Future Prospects
116(5)
References
117(4)
5 Fundamentals of AFM Cantilever Dynamics in Liquid Environments
121(36)
Daniel Kiracofe
John Melcher
Arvind Raman
5.1 Introduction
121(1)
5.2 Review of Fundamentals of Cantilever Oscillation
122(1)
5.3 Hydrodynamics of Cantilevers in Liquids
123(3)
5.4 Methods of Dynamic Excitation
126(14)
5.4.1 Review of Cantilever Excitation Methods
128(2)
5.4.2 Theory
130(1)
5.4.2.1 Direct Forcing
130(2)
5.4.2.2 Ideal Piezo/Acoustic
132(1)
5.4.2.3 Thermal
132(1)
5.4.2.4 Comparison of Excitation Methods
133(2)
5.4.3 Practical Considerations for Acoustic Method
135(2)
5.4.4 Photothermal Method
137(3)
5.4.5 Frequency Modulation Considerations in Liquids
140(1)
5.5 Dynamics of Cantilevers Interacting with Samples in Liquids
140(10)
5.5.1 Experimental Observations of Oscillating Probes Interacting with Samples in Liquids
141(1)
5.5.2 Modeling and Numerical Simulations of Oscillating Probes Interacting with Samples in Liquids
142(3)
5.5.3 Compositional Mapping in Liquids
145(3)
5.5.4 Implications for Force Spectroscopy in Liquids
148(2)
5.6 Outlook
150(7)
References
150(7)
6 Single-Molecule Force Spectroscopy
157(32)
Albert Galera-Prat
Rodolfo Hermans
Ruben Hervas
Angel Gomez-Sicilia
Mariano Carrion-Vazquez
6.1 Introduction
157(2)
6.1.1 Why Single-Molecule Force Spectroscopy?
157(1)
6.1.2 SMFS in Biology
158(1)
6.1.3 SMFS Techniques and Ranges
158(1)
6.2 AFM-SMFS Principles
159(6)
6.2.1 Length-Clamp Mode
160(3)
6.2.2 Force-Clamp Mode
163(2)
6.3 Dynamics of Adhesion Bonds
165(4)
6.3.1 Bond Dissociation Dynamics in Length Clamp
165(2)
6.3.2 General Considerations
167(1)
6.3.3 Bond Dissociation Dynamics in Force Clamp
168(1)
6.3.3.1 The Need for Robust Statistics
169(1)
6.4 Specific versus Other Interactions
169(7)
6.4.1 Intramolecular Single-Molecule Markers
170(1)
6.4.1.1 The Wormlike Chain: an Elasticity Model
170(1)
6.4.1.2 Proteins
171(3)
6.4.1.3 DNA and Polysaccharides
174(1)
6.4.2 Intermolecular Single-Molecule Markers
174(2)
6.5 Steered Molecular Dynamics Simulations
176(1)
6.6 Biological Findings Using AFM-SMFS
177(5)
6.6.1 Titin as an Adjustable Molecular Spring in the Muscle Sarcomere
177(3)
6.6.2 Monitoring the Folding Process by Force-Clamp Spectroscopy
180(1)
6.6.3 Intermolecular Binding Forces and Energies in Pairs of Biomolecules
180(1)
6.6.4 New Insights in Catalysis Revealed at the Single-Molecule Level
181(1)
6.7 Concluding Remarks
182(7)
Acknowledgments
182(1)
Disclaimer
182(1)
References
182(7)
7 High-Speed AFM for Observing Dynamic Processes in Liquid
189(22)
Toshio Ando
Takayuki Uchihashi
Noriyuki Kodera
Mikihiro Shibata
Daisuke Yamamoto
Hayato Yamashita
7.1 Introduction
189(1)
7.2 Theoretical Derivation of Imaging Rate and Feedback Bandwidth
190(2)
7.2.1 Imaging Time and Feedback Bandwidth
190(1)
7.2.2 Time Delays
191(1)
7.3 Techniques Realizing High-Speed Bio-AFM
192(8)
7.3.1 Small Cantilevers
192(2)
7.3.2 Fast Amplitude Detector
194(1)
7.3.3 High-Speed Scanner
194(2)
7.3.4 Active Damping Techniques
196(2)
7.3.5 Suppression of Parachuting
198(1)
7.3.6 Fast Phase Detector
199(1)
7.4 Substrate Surfaces
200(3)
7.4.1 Supported Planar Lipid Bilayers
200(1)
7.4.1.1 Choice of Alkyl Chains
201(1)
7.4.1.2 Choice of Head Groups
201(1)
7.4.2 Streptavidin 2D Crystal Surface
201(2)
7.5 Imaging of Dynamic Molecular Processes
203(3)
7.5.1 Bacteriorhodopsin Crystal Edge
203(1)
7.5.2 Photoactivation of Bacteriorhodopsin
204(2)
7.6 Future Prospects of High-Speed AFM
206(1)
7.6.1 Imaging Rate and Low Invasiveness
206(1)
7.6.2 High-Speed AFM Combined with Fluorescence Microscope
206(1)
7.7 Conclusion
207(4)
References
207(4)
8 Integration of AFM with Optical Microscopy Techniques
211(20)
Zhe Sun
Andreea Trache
Kenith Meissner
Gerald A. Meininger
8.1 Introduction
211(6)
8.1.1 Combining AFM with Fluorescence Microscopy
214(1)
8.1.1.1 Epifluorescence Microscopy
214(1)
8.1.2 Examples of Applications
215(1)
8.1.2.1 Ca2+ Fluorescence Microscopy
215(2)
8.1.2.2 AFM - Epifluorescence Microscopy
217(1)
8.2 Combining AFM with IRM and TIRF microscopy
217(4)
8.2.1 Interference Reflection Microscopy
217(1)
8.2.1.1 Optical Setup
218(1)
8.2.2 Total Internal Reflection Fluorescence Microscopy
218(1)
8.2.2.1 Optical Setup
218(2)
8.2.2.2 Applications of Combined AFM-TIRF and AFM-IRM Microscopy
220(1)
8.3 Combining AFM and FRET
221(1)
8.3.1 FRET
221(1)
8.3.2 FRET and Near-Field Scanning Optical Microscopy (NSOM)
222(1)
8.4 FRET-AFM
222(1)
8.5 Sample Preparation and Experiment Setup
223(8)
8.5.1 Cell Culture, Transfection, and Fura-Loading
223(1)
8.5.2 Cantilever Preparation
224(1)
8.5.3 Typical Experimental Procedure
225(1)
References
225(6)
Part II Biological Applications
231(124)
9 AFM Imaging in Liquid of DNA and Protein-DNA Complexes
233(26)
Yuri L. Lyubchenko
9.1 Overview: the Study of DNA at Nanoscale Resolution
233(1)
9.2 Sample Preparation for AFM Imaging of DNA and Protein-DNA Complexes
234(2)
9.3 AFM of DNA in Aqueous Solutions
236(3)
9.3.1 Elevated Resolution in Aqueous Solutions
236(1)
9.3.2 Segmental Mobility of DNA
237(2)
9.4 AFM Imaging of Alternative DNA Conformations
239(8)
9.4.1 Cruciforms in DNA
239(5)
9.4.2 Intramolecular Triple Helices
244(1)
9.4.3 Four-Way DNA Junctions and DNA Recombination
245(2)
9.5 Dynamics of Protein-DNA Interactions
247(6)
9.5.1 Site-Specific Protein-DNA Complexes
247(4)
9.5.2 Chromatin Dynamics Time-Lapse AFM
251(2)
9.6 DNA Condensation
253(1)
9.7 Conclusions
254(5)
Acknowledgments
254(1)
References
255(4)
10 Stability of Lipid Bilayers as Model Membranes: Atomic Force Microscopy and Spectroscopy Approach
259(26)
Lorena Redondo-Morata
Marina Ines Giannotti
Fausto Sanz
10.1 Biological Membranes
259(4)
10.1.1 Cell Membrane
259(1)
10.1.2 Supported Lipid Bilayers
259(4)
10.2 Mechanical Characterization of Lipid Membranes
263(16)
10.2.1 Breakthrough Force as a Molecular Fingerprint
263(2)
10.2.2 AFM Tip-Lipid Bilayer Interaction
265(2)
10.2.3 Effect of Chemical Composition on the Mechanical Stability of Lipid Bilayers
267(1)
10.2.4 Effect of Ionic Strength on the Mechanical Stability of Lipid Bilayers
268(3)
10.2.5 Effect of Different Cations on the Mechanical Stability of Lipid Bilayers
271(2)
10.2.6 Effect of Temperature on the Mechanical Stability of Lipid Bilayers
273(1)
10.2.7 The Case of Phase-Segregated Lipid Bilayers
274(5)
10.3 Future Perspectives
279(6)
References
279(6)
11 Single-Molecule Atomic Force Microscopy of Cellular Sensors
285(22)
Jurgen J. Heinisch
Yves F. Dufrene
11.1 Introduction
285(3)
11.1.1 Mechanosensors in Living Cells
285(1)
11.1.2 Yeast Cell Wall Integrity Sensors: a Valuable Model for Mechanosensing
286(2)
11.2 Methods
288(4)
11.2.1 Atomic Force Microscopy of Live Cells
288(2)
11.2.2 AFM Detection of Single Sensors
290(1)
11.2.3 Bringing Yeast Sensors to the Surface
291(1)
11.3 Probing Single Yeast Sensors in Live Cells
292(10)
11.3.1 Measuring Sensor Spring Properties
292(3)
11.3.2 Imaging Sensor Clustering
295(3)
11.3.3 Using Sensors as Molecular Rulers
298(4)
11.4 Conclusions
302(5)
Acknowledgments
303(1)
References
303(4)
12 AFM-Based Single-Cell Force Spectroscopy
307(24)
Clemens M. Franz
Anna Taubenberger
12.1 Introduction
307(3)
12.2 Cantilever Choice
310(1)
12.3 Cantilever Functionalization
310(1)
12.4 Cantilever Calibration
311(1)
12.5 Cell Attachment to the AFM Cantilever
311(2)
12.6 Recording a Force-Distance Curve
313(2)
12.7 Processing F-D Curves
315(2)
12.8 Quantifying Overall Cell Adhesion by SCFS
317(3)
12.9 SFCS with Single-Molecule Resolution
320(1)
12.10 Dynamic Force Spectroscopy
321(4)
12.11 Measuring Cell-Cell Adhesion
325(1)
12.12 Conclusions and Outlook
326(5)
References
327(4)
13 Nanosurgical Manipulation of Living Cells with the AFM
331(24)
Atsushi Ikai
Rehana Afrin
Takahiro Watanabe-Nakayama
Shin-ichi Machida
13.1 Introduction: Mechanical Manipulation of Living Cells
331(1)
13.2 Basic Mechanical Properties of Proteins and Cells
331(1)
13.3 Hole Formation on the Cell Membrane
332(2)
13.4 Extraction of mRNA from Living Cells
334(1)
13.5 DNA Delivery and Gene Expression
335(3)
13.6 Mechanical Manipulation of Intracellular Stress Fibers
338(5)
13.6.1 AFM Used as a Lateral Force Microscope
338(2)
13.6.2 Force Curves and Fluorescence Images under Lateral Force Application
340(1)
13.6.2.1 Case 1
340(1)
13.6.2.2 Case 2
340(3)
13.7 Cellular Adaptation to Local Stresses
343(1)
13.8 Application of Carbon Nanotube Needles
344(2)
13.9 Use of Fabricated AFM Probes with a Hooking Function
346(2)
13.9.1 Result for a Semi-Intact Cell
348(1)
13.9.2 Result for a Living Cell
348(1)
13.10 Membrane Protein Extraction
348(2)
13.11 Future Prospects
350(5)
Acknowledgments
350(1)
References
350(5)
Index 355
Arturo M Baró has spent most of his career at the Universidad Autonoma of Madrid and has been working in the fi eld of Surface Physics and Nanoscience. In 1983, he spent one year at the IBM Research Lab in Zürich where he worked with Professors Rohrer and Binnig, who discovered STM. He is the author of 160 publications with a citation index h = 38. In 1985, he founded the company NANOTEC ELECTRONICA, S.L., which is dedicated to the fabrication and sale of AFM machines. He has been honored with the research prizes from the Humboldt Foundation.

Ronald G. Reifenberger has been on the faculty at Purdue University, W. Lafayette, USA since 1978. Following his PhD in physics from the University of Chicago, he was a post-doctoral fellow at the University of Toronto, Canada. His nanophysics laboratory at Purdue uses innovative experimental techniques to examine nanoscale properties of matter. His research focus since 1985 has been primarily scanning probe microscopy. Reifenberger is currently the director of the Kevin G. Hall Nanometrology Laboratory in the Birck Nanotechnology Center at Purdue.