xxxxxxxxxxxxx Scanning Probe Microscopes xxxxxxxxxxx
xxxxxxxxxxx SCANNING


MICROSCOPES xxxxxxxx(STM--AFM--FFM)xxxxxxxxxxxx

xxxxxxxxxxxx K. S. B I R D I xxxxxxxxxxxx2003xxxxxx
xxxxxxxxxxxApplications in Science and Technologyxxxx
xxxxxCRC PRESS xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxBoca Raton London New York Washington, D.C.xxxxxxxx
xxxxxxxxC O N T E N T S xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
1 - Introduction
2 - Scanning Probe Microscopes (SPMs)
3 - Lipid-Like Molecules on Solids and SAMs
4 - Biopolymers and Synthetic Polymers Structures by STM and AFM
5 - Crystal Structures by STM and AFM
6 - Studies of Solid Surfaces by SPMs
7 - Diverse Applications of SPMs (STM and AFM, etc.) and Nanotechnology

xxxxxxxxxxxxxxDedication:::: to.......
xxxxxxxxxxxxxxxxxxxLilian, Leon, and Esma xxxxxxxxxx


Mankind has always been keen about being able to see through the microscope, in order to
understand all kinds of natural phenomena. The degree of resolution of microscopes has indeed
increased over the decades from a few hundred to almost a million times. The latter techniques
like the electron microscope allowed one to be able to see with molecular resolution.
However, only two decades ago a new technique was invented, the scanning probe microscope (SPM),
which revolutionized the whole microscopy application area. Actually the first type was based on
scanning tunneling microscopy (STM), which resulted in the award of Nobel prize. Some years later
atomic force microscope (AFM) was added to these SPMs. SPMs thus allowed one to see and analyze
molecules under ambient laboratory conditions. Later, one could even investigate under fluids
(later under high pressure or vacuum). The three-dimensional (digital) images could be analyzed
by digital procedures, thus enhancing the analyses. Under dynamic conditions one can see live
molecular details, such as gas adsorption.

The aim of this book is to guide the reader through the vast developments of SPMs which have
taken place over the last decades. STM and AFM both have been found to provide useful information
at molecular level of all kinds of molecules (small molecules [inorganic or organic compounds or
lipid-like substances]; macromolecules [biopolymers; cells; viruses]). Besides STM and AFM, recently
new dimensions have been added. This latter development has introduced a new term in the industrial
revolution, the so-called nanotechnology. Nanotechnology, is called the science and technology of
precisely controlling the structure of matter at the molecular level. Without any doubt, this is widely
viewed as the most significant technological frontier currently being explored. Materials and devices
at the nanoscale (a nanometer is one billionth of one meter: or roughly a thousandth of the thickness
of this sheet of paper in the book) hold vast promise for innovation in virtually every industry and
public endeavor including health, electronics, transportation, the environment and national
security, and have been heralded as “the next industrial revolution.”

The book starts with an introduction to the development of SPMs. The basics of STM and AFM
are described. The other SPMs (friction force microscope (FFM), SNOM) are also described. The
different apparatus are described and the method of calibration is delineated besides other
parameters, along with extensive references and experimental details.

The rest of the book is divided into chapters related to different kinds of molecular species
and systems from real life. The lipid-like molecules are described under a separate chapter. This
includes the vast area of research which is going on about the self-assembly monolayers (SAMs). The
contribution of SPMs to the understanding of SAMs has been immense, since this has provided information
in three-dimensions, for the first time in literature. The subject of SAMs is becoming a vast application
area in both industry (micro-electronics; computer chips) and biological (vesicles; sensors) applications.

The SPM's application to the understanding of macromolecules is described under a separate chapter. The
very first image of DNA was actually obtained by using SPM. Later, other biological molecules were
investigated (both by STM and AFM), and are described in detail. The experimental procedures are
extensively described. SPMs also provide dynamics of various systems, such as the rates of reactions
or adsorption on surfaces. SPMs also are found to provide information of reactions which take place in nanoreactors.

The nanotechnoloigical developments are very extensive and are described accordingly in much detail. These
subjects include nanolithography and other applications. The developments around friction force microscopy (FFM)
are described in detail.

The main theme in the book has been to provide systematic and in-depth experimental details covering the various
aspects of SPM applications in science and technology (nanotechnology). Nanotechnology has been given high
priority support from all the national science foundations worldwide. The reader can thus easily
determine the experimental conditions and thus follow these with a vast number of pertinent references. This
is an attempt to help the reader in designing his own experiments to almost all kinds of applications of these SPMs.

The aim of this book thus has been to provide basic and advanced information, hitherto not easily available in
one volume. The chapters are arranged in such a way that it can be used as a textbook about SPMs. Further, the
extensive information provided is also useful to advanced researchers in this field. The book is even more useful
for a beginner, since the detailed data and description of various applications will guide one through the extensive literature covered.

Additionally, there are presented data in the form of two- and three-dimensional figures, wherever these are
pertinent. This is intended to provide an impressive image gallery to the reader, which should present a clear
view of the application posibilities of SPMs to science and technology.
Auger electron spectroscopy
Atomic force microscope/microscopy
Atomic sensitivity factor
Attenuated total relection
Bilipid membranes
Bridging model
Corona discharge
Contact electrification
Chemical force microscopy
Conducting probe atomic force microscopy
Cyclic voltammogram
Dipping force microscope
Dynamic secondary ion mass spectrometry
Energy-filtered analytical transmission electron microscopy
Electron microscope/microscopy
Electrochemical quartz crystal microbalance
Field-emission gun scanning electron microscopy
Field-emission scanning electron microscopy
Friction force microscope
Fast Fourier transform
Frequency modulation
Fourier transform infrared spectroscopy
Highly oriented pyrolytic graphite
High-resolution electron microscopy
High-resolution transmission electron microscopy
Inverted chemical force microscopy
Isoelectric point
Low-energy electron diffraction
Lateral force microscope
Laser reflection detection system
Magnetic force microscope
Mean patch diameters
Mass spectrometry
Nanoelectromechanical systems
Nuclear magnetic resonance
Octadecyl trichlorosilane
Probe beam deflection
Patch charge model
Photon correlation spectroscopy
Position sensitive detector
Phase-volume (adj.)
Point-of-zero charge
Quartz crystal microbalance
Quasielectric light scattering
Reverse high energy electron diffraction
Reactive ion etching
Self-assembly monolayer
Scanning capacitance microscopy
Scanning electron microscope
Scanning electron microscope with polarization
Scanning electric potential microscopy
Surface force apparatus
Surface force microscope
Shear force microscope
Secondary ion mass spectrometry
Scanning near-field optical microscopy
Scanning near-field optical microscopy and atomic force microscopy
Scanning probe microscope
Surface plasmon resonance spectroscopy
Scanning tunneling microscope
Signal-to-noise ratio
Scanning transmission x-ray microscopy
Small unilamellar vesicles
Transverse dynamic force microscopy
Transmission electron microscope
Tapping-mode atomic force microscopy
Ultrahigh vacuum
X-ray photoelectron spectroscopy
Chapter 1
1.1 Background
1.2 History of Microscopy
1.2.1 Optical Microscopy
1.2.2 Electron Microscopy
Chapter 2
Scanning Probe Microscopes (SPMs)
2.1 Scanning Tunneling Microscope (STM)
2.1.1 STM Apparatus
2.1.2 Description of STM
2.2 Electron Tunneling
2.3 Atomic Force Microscope (AFM)
2.3.1 Basic Principles of AFM
2.3.2 Imaging in AFM and Tip Effects
2.3.3 Analyses of Tip Effects
2.3.4 Effects Related to Thermal Drift
2.3.5 Effect of Mechanical Vibrations
2.4 Modes of Operation of AFM
2.5 Simultaneous AFM and Scanning Near-Field Fluorescence (SNOM and SNOM-AFM)
2.6 Friction Force Microscopy (FFM)
2.6.1 Forces in AFM Van der Waals Forces Electrostatic Force Hydrophobic Forces Double-Layer Force
2.7 STM and AFM Studies under Fluids
2.8 Sample Preparation Procedures for STM and AFM
2.8.1 Substrates
2.8.2 Diverse Substrates
2.8.3 Langmuir-Blodgett (LB) Films
2.8.4 Biopolymer Samples
2.8.5 STM and AFM Analyses of Electron Microscope Grids
2.9 Calibration and Image Analysis of STM and AFM
2.10 Comparative Studies of Diverse Molecules by STM and AFM
Chapter 3
Lipid-Like Molecules on Solids and SAMs
3.1 Collapsed Lipid Monolayers (Self-Assembly)
3.1.1 Mg-Stearate Films
3.1.2 Cholesterol and Other Oxidized Cholesterol Films
3.1.3 Mixed Lipid Monolayers
3.2 Domain Patterns in Monomolecular Film Assemblies
3.2.1 Macrodomains
3.2.2 Theoretical Analysis of Domains (Macrodomains) Domains (Macro- and Nano-Size) Shape
3.3 Mixed Lipid Molecule Assemblies
3.4 Holes in LB Films of Self-Assembly Monolayers
3.5 Visualization of Vesicles by AFM
3.5.1 DPPC-Cholesterol (1:1 Molar) SUVs
3.6 LB Films of Liquid Crystals
3.7 STM and AFM Studies of Diverse Molecules on Solids
3.7.1 Studies of Diverse Small Molecules
3.7.2 Surfactant Molecules Studies by AFM
3.7.3 C60 Monolayers
3.7.4 Preparation of C60 Deposits for Electrochemical Studies
3.7.5 Voltammetry of Solid C60 Mechanically Attached to a Graphite Electrode
3.7.6 Benzene and Phenyl Radicals on Metal Surfaces
3.7.7 Other Diverse Systems
3.8 STM Studies on the Effect of Functional Group
Chapter 4
Biopolymers and Synthetic Polymers Structures by STM and AFM
4.1 DNA Structures by STM and AFM
4.2 SPM Studies of Three-Dimensional Protein Structures
4.2.1 Catalase
4.2.2 Other Protein Molecules
4.2.3 Pectin AFM Analyses
4.3 Protein Adsorption Studies by AFM
4.4 Biological Macromolecular Structures
4.4.1 Studies of Virus and Cell Structures by SPMs
4.5 Synthetic Polymers Studies by SPMs
4.5.1 Dextran Molecule
4.5.2 Single Macromolecule Adsorption Studies
4.5.3 Latex Particle Analyses by AFM
4.5.4 Other Diverse Polymers
4.5.5 Diverse Properties of Synthetic Polymers Determination of Thickness of Spin-Cast Polymer Thin Films AFM Tip-Scratch Method
4.5.6 Polymerization in Monolayers as LB Films
4.5.7 Single-Molecule Force Spectroscopy
4.5.8 Mechanical Deformation Studies by AFM of Synthetic Polymers The Detachment of a Polymer Chain from a Weakly Adsorbing Surface Using an AFM Tip
4.5.9 AFM Studies of Polymers by Force Modulation Methods
4.6 Mixed Monolayers of Macromolecules and Lipids
4.6.1 Hemoglobin Molecular Morphology by AFM
4.6.2 POE+SDS
4.6.3 Mixed SDS+Gelatin on HOPG
4.7 Diverse Macromolecular Properties as Studied by SPMs
4.7.1 Electron Transfer (ET) Studies by AFM
4.7.2 Other Diverse Macromolecules Xanthan Immunoglobulin G (IgG) Gramicidin and Other Ionophores Mixed Monolayers of Virus Cell or Fusion Peptide Cell
4.8 Monolayers of Synthetic Polyamino Acids
4.9 Biopolymer SAM Structures at Interfaces by STM and AFM
4.9.1 Determination of the Surface Potential of Crystals of Biopolymers by AFM
4.9.2 Molecular Recognition of Biomolecules by AFM
4.9.3 Applications of Transverse Dynamic Force Microscopy (TDFM) and AFM to Membranes Microscopy
Chapter 5
Crystal Structures by STM and AFM
5.1 Crystal Structures of Small Molecules
5.1.1 Morphology of Crystals of Different Amino Acids by AFM Studies
5.2 Surface Adsorption Studies by SPMs
5.2.1 Studies of Chiral Compounds by AFM
5.3 Macromolecule Crystals by STM and AFM
5.3.1 Crystallization and AFM Investigation of a Polymer Structure
Chapter 6
Studies of Solid Surfaces by SPMs
6.1 Wetting Properties of Solid Surfaces
6.2 AFM Analyses of Surface Acid-Base Properties
6.3 Measurement of Attractive and Repulsive Forces by Atomic Force Microscope (AFM)
Chapter 7
Diverse Applications of SPMs (STM and AFM, etc.) and Nanotechnology
7.1 STM and AFM in Organic Chemistry
7.1.1 Imaging Liquid Crystals by SPMs
7.1.2 Tunneling Mechanism through Organic Materials Conducting Probe Atomic Force Microscopy (CP AFM)
7.2 Semiconductor Study by SPM
7.2.1 Composite Materials Investigations by SPMs
7.3 STM and AFM in Inorganic Chemistry
7.3.1 Corrosion Phenomena Studies by SPMs
7.3.2 Diverse Systems
7.3.3 Silica Particle Size and Shape Analyses
7.4 Nanolithography and Nanomachining
7.4.1 Atomic Switch (Nanoscale) by STM
7.4.2 Solid Surface Manipulation at Molecular Scale
7.5 Qualitative and Quantitative Analyses at Nanoscale
7.6 Application of SPMs under Dynamic Conditions
7.6.1 STM Studies of Adsorption of Gas on Solid Surfaces
7.7 Application of AFM to Immunodiagnostic Systems
7.8 Applications of STM and AFM in Industry
7.8.1 Domain Images by Scanning Force Microscopy (SFM)
7.8.2 Glassy Carbon (GC) Electrodes
7.8.3 Blister Formation
7.9 SPM Studies of Nanoscale Reactors
7.9.1 Self-Assembled Monolayer Structure
7.9.2 In Situ AFM Imaging of SAMs during Hydrolysis
7.10 Nanoscale Evaluation of Surface Roughness by SPMs
7.11 Application of STM and AFM in Pollution Control
7.12 Friction Force Microscope (FFM)
7.13 Time-Resolved Analyses by STM
305 pagesxxxxxxxxxxxxxxxxxx

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