Introduction to Scanning

Tunneling Microscopy
Second Edition

C. Julian Chen
Department of Applied Physics and Applied Mathematics
Columbia University, New York

OXFORD
UNIVERSITY PRESS
MONOGRAPHS ON THE PHYSICS AND CHEMISTRY OF MATERIALS

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Statistical physics of fracture and breakdown in disordered systems B. K. Chakrabarti
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Electronic processes in organic crystals and polymers (Second edition) M. Pope and
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Introduction to scanning tunneling microscopy (Second edition) C. J. Chen

istm: “prelims” — 2007/7/19 — 17:54 — page ii — #2

 Preface to the Second Edition

In a 1959 speech entitled There’s Plenty of Room at the Bottom [1], Richard
Feynman invited scientists to a new field of research: to see individual atoms
distinctly, and to arrange the atoms the way we want. Feynman envisioned
that, by achieving those goals, one could synthesize any chemical substance
that the chemist writes down, resolve many central and fundamental prob-
lems in biology at the molecular level, and dramatically increase the density
of information storage. Some 20 years later, those goals began to be achieved
through the invention and application of the scanning tunneling microscope
(STM) [2, 3] and the atomic force microscope (AFM) [4]. The inventors of
STM, two physicists at IBM Research Division, Gerd Binnig and Heinrich
Rohrer, shared the 1986 Nobel Prize in physics [5, 6].
At that time, I was fortunate to be in the Department of Physical Sci-
ences of IBM Research Division, and had the opportunity to design, build,
and run those fascinating instruments. Partially based on my personal ex-
perience and understanding, in 1993, the first edition of this book was pub-
lished [7]. In the decade following, Feynman’s foresight has grown into a
vast field of research, nanoscience and nanotechnology. As a result, tremen-
dous advances have been achieved in the understanding of the basic physics
as well as instrument design and operation of STM and AFM. It is time to
publish a second edition to include those recent advances, and to satisfy the
urgent need for an updated, unified, accurate, and pedagogically assessable
textbook and reference book on STM and AFM.
During the years of 1994 to 2003, I was concentrating on the research
of human voice and languages, which were my favorite subjects ever since
my college years. And I received more corporate recognition than for my
basic research in physics [8]. However, the news about the advancements in
STM and AFM constantly called me to come back to nanoscience and nan-
otechnology. In December 2003, I received a kind invitation from Professor
Roland Wiesendanger, the Director of the Institute of Applied Physics at
Hamburg University, to become a guest scientist. This is one of the largest
and most productive centers of STM and AFM research, especially in spin-
polarized STM and non-contact AFM. And for the first time in my life,
I could concentrate 100% of my time on nanoscience and nanotechnology
research. In the summer semester of 2005, in a graduate-level course in
nanostructure physics jointly given to the Department of Physics and the
Department of Chemistry at Hamburg University, Professor Roland Wiesen-
danger lectured the analyses of various nanostructures, and I lectured the
principles and instrumentation of STM and AFM. The lecture notes on STM
and AFM then became the blueprint of the second edition of the STM book.
Following are some examples of the additions to the second edition:
Atomic force microscopy, with a refined frequency-modulation mode,
ii Chen: Introduction to Scanning Tunneling Microscopy

has achieved true atomic resolution in the attractive atomic force regime,
often referred to as the non-contact AFM. In some cases, its resolution
has even surpassed that of STM. The observed bias-dependence of atomic
forces provides information about the details of electronic structure. This
new technique enables atomic-scale imaging and characterization not only
for conductors, but also for insulators.
Significant breakthrough in spin-polarized STM has enabled the observa-
tion of local magnetic phenomena down to atomic scale. Such advancement
was to drive the development of nanomagnetism, which would have deep
impact on the technological applications of magnetism.
Inelastic electron tunneling spectroscopy (IETS), initially discovered in
metal-insulator-metal tunneling junctions to observe vibrational frequen-
cies of embedded molecules, was advanced to STM junctions, enabling the
observation of vibrational states of individual molecules. The successful
demonstration of STM-IETS elevated the field of single-molecule chemistry
to an unprecedented level.
At the time that the first edition was written, atom manipulation was
still a highly specialized personal art. In the later years, the underlying
physics has gradually been discovered, and the atom-manipulation process is
becoming a precise science. Besides single atoms, molecules are also subject
to manipulation. It was often said that STM is to nanotechnology what
the telescope was to astronomy. Yet STM is capable of manipulating the
objects it observes, to build nanoscale structures never existed in Nature.
No telescope is capable of bringing Mars and Venus together.
In the process of further improving the resolution of STM and AFM,
the understanding of its basic physics has been advanced. Numerous con-
vincing theoretical and experimental studies have shown that the imaging
mechanism of both STM and AFM at atomic resolution can be understood
as a sequence of making and breaking of partial covalent bonds between
the anisotropic quasi-atomic orbitals on the tip and those on the sample.
The nature of STM and AFM, including those with spin-polarized tips, can
be understood with a unified perspective based on Heisenberg’s concept of
resonance in quantum mechanics.
Commercialization of STM and AFM has been greatly advanced. Owing
to the rapidly expanding research in nanotechnology, especially in molecular
biology and in materials science, AFM with tapping mode operating in air
or in liquid now constitutes the largest market share. Therefore, a brief
presentation of its basic principles is included.
In spite of the availability of commercial STMs and AFMs, research
groups worldwide continue to design and build customized instruments to
achieve advanced features and to serve special experimental needs. Often,
those new designs are then adapted by instrument manufacturers to become
products. Although the basic principles of the design and construction
of STM and AFM was laid down in the second part of the first edition,

Copyright 2008 Oxford University Press

 Chen: Introduction to Scanning Tunneling Microscopy iii

Instrumentation, new trends and ideas have been added.

The basic organization of the second edition is essentially identical to
the first edition. All the materials in the first edition proven to be useful are
preserved. Some of the less important materials are eliminated or converted
to Problems at the ends of various chapters. The first chapter, Overview,
is preserved but updated. Several recent applications of STM and AFM,
probably of interest to general readers, are added. The title of the first Part
is changed to Principles from Imaging Mechanism because of the inclusion
of the physics of atom and molecule manipulation. The Gallery of STM
Images is updated, with more historical photos and AFM images added,
which is now entitled simply Gallery. To preserve the classical style of the
first edition and to reduce the cost of printing, all photographs and images
are in black-and-white. Similar to the first edition, only a few illustrative
applications of STM and AFM are presented, because there are already
many excellent books on various applications. For example, the monograph
Scanning Probe Microscopy and Spectroscopy: Methods and Applications by
R. Wiesendanger [9]; the book series Scanning Tunneling Microscopy I, II,
and III edited by R. Wiesendanger and H.-J. Güntherodt [10]; Scanning
Tunneling Microscopy edited by J. A. Stroscio and W. J. Kaiser [11]; the
second edition of the monograph Scanning Tunneling Microscopy and its
Applications by C. Bai [12]; and the second edition of Scanning Probe Mi-
croscopy and Spectroscopy: Theory, Techniques, and Applications edited by
D. Bonnell [13]. Similar to the first edition, to ensure pedagogical soundness,
the focus is on simple but useful theories, with every derivation presented in
full detail. Many new figures are added to illustrate the concepts in physics.
In the second edition, care has been taken to use SI units as much as pos-
sible. That would provide a unified order-of-magnitude mental picture of
the physical quantities involved. Because of the enormous growth of the
size of literature, the reference list at the back of the second edition only
includes those cited by the text, selected and arranged automatically by La-
TeX. In the age of the Internet, exhaustive reference lists can be obtained
by searching on the web.
The author is deeply grateful to H. Rohrer for commenting extensively on
the manuscript of the first edition, and publicly recommending the book to
newcomers as well as experts. The author is equally grateful to Ch. Gerber,
an architect of both the first STMs and the first AFMs, for comments on the
second edition, and especially for providing a number of precious original
photographs and images of historical interest. An early manuscript of the
second edition was thoroughly reviewed by a number of experts in that field.
Corrections and improvements were made upon their comments. Following
is an incomplete list. The entire book by K.-H. Rieder of Swiss Federal
Laboratories for Materials Research. Part I and Chapter 15 by R. Pérez
of Universidad Autonoma de Madrid. Part II, especially Chapter 15, by
F. Giessibl of University of Regensburg. All chapters related to scanning

Copyright 2008 Oxford University Press

iv Chen: Introduction to Scanning Tunneling Microscopy

tunneling spectroscopy and spin-polarised STM by O. Pietzsch of Hamburg

University. The main part of Chapter 1 and Chapter 12 by F. Besenbacher,
J. V. Lauritsen, and E. Laegsgaard of University of Aarhus. Chapter 9
by W. Coburn and P. Stokes of EBL Products, Inc., and M. Ordillas of
Morgan Electro Ceramics, Inc. Chapter 14 by R. Feenstra of Carnegie
Melon University. Chapter 15, especially Section 15.4, by C. Prater of Veeco
Instruments Inc. Section 1.5.2 and Section 13.6 by the group of J. Ulstrup
of Technical University of Denmark. Section 1.5.4 by J. Hu of Jiaotong
University, Shanghai. Section 13.3.5 by R. A. Wolkow of University of
Alberta. Last but not least, Sections 5.2.1, 5.2.2, and 5.2.3 by W. Hofer of
University of Liverpool.
The Gallery is an integrated part of the book. The author is indebted
to the following authors who contributed high-resolution black-and-white
original photographs and images for the publication of this book: Plates 2,
3, and 4, Ch. Gerber. Plate 5, R. Wiesendanger. Plates 7, 11, 12, and 16,
J. Boland. Plates 8, 10, and 15, R. Feenstra. Plate 9, J. V. Barth. Plate 13,
D. J. Thomson. Plate 14, J. Repp and G. Meyer. Plate 17, M. Bode. Plate
18, L. Berbil-Bautista. Plate 19, O. Pietzsch. Plate 20, A. R. Smith. Plates
21 and 22, S. Fölsch. Plate 23, K. F. Braun. Plates 24, P. Weiss. Plate 25,
C. F. Hirjibehedin. Plate 27, F. J. Giessibl. Plate 28, J. V. Lauritsen and F.
Besenbacher. Plate 29, R. Pérez and Ó. Custance. Plate 30, Ó. Custance.

C. Julian Chen

Columbia University
in the City of New York

July 2007

Copyright 2008 Oxford University Press

 Gallery

Historical photographs
Plate 1. The IBM Zurich Laboratory soccer team
Plate 2. A humble gadget that shocked the science community
Plate 3. The creators of the atomic force microscope
Plate 4. The first atomic force microscope
STM studies of surface structures
Plate 5. ‘Stairway to Heaven’ to touch atoms
Plate 6. Zooming into atoms
Plate 7. Underneath the Si(111)-7×7 surface
Plate 8. STM image of a GaN(0001̄) surface √
Plate 9. Large-scale image of the Au(111)-22× 3 structure
Plate 10. Large-scale image of the Ge(111) surface
Plate 11. Details of the Ge(111)-c(2×8) surface
Molecular orbitals and chemistry
Plate 12. Individual π and π ∗ molecular orbitals observed by STM
Plate 13. Organic molecules observed by STM
Plate 14. Observation of the HUMO and LOMO of an organic molecule
Plate 15. Voltage-dependent images of the Si(111)-2×1 surface
Plate 16. Chemical vapor deposition of the Si(100) surface
Spin-polarized STM
Plate 17. SP-STM images of an Fe island
Plate 18. SP-STM images of Dy films
Plate 19. SP-STM studies of nanoscale Co islands on Cu(111)
Plate 20. SP-STM studies of antiferromagnetic crystal Mn3 N2
Atom manipulation
Plate 21. Construction of Cun chains by atom manipulation using STM
Plate 22. Quantum states observed on Cun chains
Plate 23. The triangular quantum corral
Plate 24. Manipulating hydrogen atoms underneath palladium surface
Plate 25. An artificial atomic-scale rock garden
Atomic force microscopy
Plate 26. Si(111)-7×7 structure resolved by AFM
Plate 27. Current images and higher-harmonics force images on graphite
Plate 28. Tip dependence of non-contact AFM images of TiO2
Plate 29. Chemical identification of individual surface atoms using AFM
Plate 30. Atom manipulation using AFM
2 Chen: Introduction to Scanning Tunneling Microscopy

Plate 1. The IBM Zurich Laboratory soccer team. On October 15,

1986, the soccer team of IBM Zurich Laboratory and Dow Chemical played
a game which had been arranged earlier. To everyone’s surprise, a few hours
before the game, the Swedish academy announced the Nobel Prize for Gerd
Binnig (right, holding flowers) and Heinrich Rohrer (left, holding flowers).
Newspaper reporters rushed in for a press conference.
Towards the end of the press conference, Binnig and Rohrer said that
they must leave immediately because both were members of the laboratory
soccer team. The reporters followed them to the soccer field. A photogra-
pher for the Swiss newspaper Blick took this photograph before the game
started. At the center of the photograph, holding a soccer ball is Christoph
Gerber, responsible for building the first scanning tunneling microscope as
well as the first atomic force microscope.
(Original photograph by courtesy of IBM Zurich Laboratory.)

Copyright 2008 Oxford University Press

 Chapter 1
Overview

1.1 The scanning tunneling microscope

The scanning tunneling microscope (STM) was invented by Binnig and

Rohrer and implemented by Binnig, Rohrer, Gerber, and Weibel [2, 3].
Figure 1.1 shows its essential elements. A probe tip, usually made of W
or Pt–Ir alloy, is attached to a piezodrive, which consists of three mutually
perpendicular piezoelectric transducers: x piezo, y piezo, and z piezo. Upon
applying a voltage, a piezoelectric transducer expands or contracts. By ap-
plying a sawtooth voltage on the x piezo and a voltage ramp on the y piezo,
the tip scans on the xy plane. Using the coarse positioner and the z piezo,
the tip and the sample are brought to within a fraction of a nanometer each
other. The electron wavefunctions in the tip overlap electron wavefunctions
in the sample surface. A finite tunneling conductance is generated. By ap-
plying a bias voltage between the tip and the sample, a tunneling current
is generated. The concept of tunneling will be presented in Section 1.2.

Fig. 1.1. The scanning tunneling microscope in a nutshell. The scanning

waveforms, applying on the x and y piezos, make the tip raster scan on the sample
surface. A bias voltage is applied between the sample and the tip to induce a tunneling
current. The z piezo is controlled by a feedback system to maintain the tunneling current
constant. The voltage on the z piezo represents the local height of the topography. To
ensure stable operation, vibration isolation is essential.
24 Chen: Introduction to Scanning Tunneling Microscopy

The most widely used convention of the polarity of bias voltage is that
the tip is virtually grounded. The bias voltage V is the sample voltage. If
V > 0, the electrons are tunneling from the occupied states of the tip into
the empty states of the sample. If V < 0, the electrons are tunneling from
the occupied states of the sample into the empty states of the tip.
The tunneling current is converted to a voltage by the current amplifier,
which is then compared with a reference value. The difference is amplified
to drive the z piezo. The phase of the amplifier is chosen to provide a
negative feedback: if the absolute value of the tunneling current is larger
than the reference value, then the voltage applied to the z piezo tends to
withdraw the tip from the sample surface, and vice versa. Therefore, an
equilibrium z position is established. As the tip scans over the xy plane, a
two-dimensional array of equilibrium z positions, representing a contour plot
of the equal tunneling-current surface, is obtained, displayed, and stored in
the computer memory.
The topography of the surface is displayed on a computer screen, typi-
cally as a gray-scale image, see Fig. 1.2(a). The gray-scale image is similar
to a black-and-white television picture. Usually, the bright spots represent
high z values (protrusions), and the dark spots represent low z values (de-
pressions). The z values corresponding to the gray levels are indicated by
a scale bar. For a more quantitative representation of the topography, a
contour plot along a given line is often provided, as shown in Fig. 1.2(b).
The most convenient unit for x and y is nanometer (nm, 10−9 m), and the
most convenient unit for z is picometer (pm, 10−12 m).
To achieve atomic resolution, vibration isolation is essential. This is
achieved by making the STM unit as rigid as possible, and by reducing the
influence of environmental vibration to the STM unit. See Chapter 10.

Fig. 1.2. Gray-scale image and contour plot. (a) A 5nm×5nm gray-level to-
pographic image of Si(111)7×7. The bright spots represent protrusions, and the dark
spots represent depressions. The z values corresponding to the gray levels are indicated
by a scale bar. (b) The topographic contour along a line in (a), for a more quantitative
representation. By courtesy of F. Giessibl.

Copyright 2008 Oxford University Press

 Chen: Introduction to Scanning Tunneling Microscopy 25

1.5 Illustrative applications

Over the last decades, the applications of STM and AFM have grown so
fast and so vast that a thorough review would take many volumes. And
there are already many good books as well as review articles published
on applications of STM and AFM in various fields. In this section, a few
examples are presented as illustrations.

1.5.1 Catalysis research

Catalysis is the backbone of synthetic chemistry. It is a basic process in
the production of fabrics, fuels, fertilizers and pharmaceuticals. Catalysis
is also essential in environmental protection. For example, required by law,
each automobile must have a catalytic converter to remove toxic exhaust
gases, notably CO and NOx . Although it is well known that catalytic
reactions often take place at specific active atomic sites on the catalyst
surface, the research in catalysis have been mainly relying on test-and-
error experimentation involving macroscopic parameters. The invention
of STM enables detailed studies of the electronic structures of the active
sites at catalyst surfaces. STM can even operate in an atmosphere with
actual reactants, thus to observe the transformation of molecules at active
atomic sites on real time. Therefore, STM research can help facilitate a full
understanding and control of the constituents at the molecular and atomic
levels, and to open up the possibility of designing the catalysis process at
the single molecule level [14]. Here are two examples.

Ni-Au catalyst for steam reforming

Steam reforming is a method in the chemical industry to produce hydrogen
from hydrocarbons. For example, in the presence of a catalyst, alkanes react
with steam (overheated water vapor) to generate H2 and CO:

Cn H2n+2 + nH2 O → n CO + (2n + 1) H2 . (1.1)

The most important case is the reaction of methane with steam,

CH4 + H2 O → CO + 3 H2 . (1.2)
It is the most common and least expensive method to produce hydro-
gen. The typical catalyst is nickel nanoclusters supported on a MgAl2 O4
substrate. Nevertheless, in parallel with the steam reforming process, nickel
also catalyzes the production of graphite, which impedes the activity due to
the formation of a blocking carbon layer on the nickel surface (coking) and
may eventually lead to the breakdown of the catalyst. An existing solution
to that problem is by mixing a minute amount of H2 S to the reactants,
which poisons the nickel catalyst. Because sulfur poisons the formation of

Copyright 2008 Oxford University Press

26 Chen: Introduction to Scanning Tunneling Microscopy

graphite more than it poisons the steam formation reaction, the lifetime of
the catalyst is prolonged. However, the overall rate is lower, and the inclu-
sion of H2 S is harmful to the subsequent processes and the environment.
A new idea comes from the STM studies of the Ni-Au system [15]. Ni
and Au are immiscible in the bulk. No binary alloy can be formed. How-
ever, STM studies showed that by mixing a few percents of Au to Ni, after
annealing at 800 K, a surface binary alloy is formed: many Ni atoms on the
surface are substituted by Au atoms, see Fig. 1.3. The topographic STM
image shows that as if the Au atoms are darker (deeper), and the Ni atoms
immediately adjacent to an Au atom are brighter (higher). It is not because
the Au atoms are depressed and the adjacent Ni atoms are protruded, but
is an electronic effect inherent to STM. According to the Tersoff-Hamann
model of STM imaging [16, 17] (see Chapter 6), a topographic STM image
is the contour of equal Fermi-level local density of states of the sample,
measured at the center-of-curvature of the tip r0 , ρ(EF , r0 ). On the Au
atoms, the value of ρ(EF , r) is lower than that of the normal Ni atoms. On
the other hand, the value of ρ(EF , r) of a Ni atom adjacent to a Au atom
is higher owing to the perturbation by the Au atom. For a Ni atom with
two Au neighbors, the perturbation is even stronger, see Fig. 1.3. Because
the Fermi-level local density of states is closely related to catalytic reactiv-
ity, those Ni atoms provide a higher reactivity than the normal Ni atoms.
Furthermore, the carbon atoms are much less likely to adsorb on the Ni
atoms adjacent to a Au atom. The results are: by mixing a few percents
of Au to Ni, the reactivity of the steam formation process is enhanced, and

Fig. 1.3. STM topographical images of the Ni-Au system. (a) An image of
Ni(111) with 2% Au. The Au atom appears as depressions because of the LDOS at the
Fermi level is lower. The Ni atoms surrounding an Au atom appear as protrusions because
of the enhancement of LDOS at the Fermi level, indicating a higher chemical reactivity.
For the Ni atom between two Au atoms, the LDOS enhancement is even higher. (b) An
image of Ni(111) surface with 7% of Au. The number of Ni atoms with doubly enhanced
Fermi-level LDOS is increased. (Original figure in black-and-white with high resolution
by courtesy of F. Besenbacher and J. V. Lauritsen. Reproduced with permission [15].
Copyright 1998 the American Association for the Advancement of Science.)

Copyright 2008 Oxford University Press

 Chen: Introduction to Scanning Tunneling Microscopy 27

Fig. 1.4. Conversion rates of the Ni catalyst and the Ni-Au catalyst. The con-
version rates of steam reformation of n-butane and water vapor using different catalysts.
Gray curve: pure Ni catalyst. the rate deteriorates with time as a result of the parasitic
graphite formation process. Black curve: Ni-Au catalyst, which shows no deterioration
of reaction rate. (Original figure in black-and-white with high resolution by courtesy of
F. Besenbacher and J. V. Lauritsen. Reproduced with permission [15]. Copyright 1998
the American Association for the Advancement of Science.)

the graphite formation process is reduced. While the conversion rate of the
pure Ni catalyst decreases markedly after an hour of operation, the conver-
sion rate of Ni-Au catalyst remains constant. Therefore, the Ni-Au catalyst
could be active for a much longer time, see Fig. 1.4.
Based on the STM study, a new catalyst, with about 16.5 weight percents
of Ni and 0.3 weight percents of Au on a MgAl2 O4 matrix, is designed, which
substantially improves the steam formation process.

Understand and improve the MoS2 catalyst

Petroleum contains a wide range of sulfur compounds, for example, alka-
nethiol (Cn H2n+1 SH) and thiophene (C4 H4 S). Sulfur is harmful for the
chemical processings and for the environment. The process to remove sulfur,
hydrodesulphurization (HDS), is an essential step in petrochemical industry.
The typical catalyst is molybdenum disulfate (MoS2 ). In the presence of
hydrogen, the HDS reaction converts alkanethiol into alkane,

Cn H2n+1 SH + H2 → Cn H2n+2 + H2 S, (1.3)

and the gas-phase H2 S is easily removed.

MoS2 is a layered material, similar to graphite. The bulk of MoS2 con-
sists of thin sheets of S-Mo-S sandwiches, and those sheets are held together
by van der Waals forces. The basal planes of MoS2 are chemically inert.
Therefore, catalytic reactivity must reside in the rims of the sheets. How-
ever, before the application of STM, the preferred structure and the active
sites of MoS2 crystallites, as well as the reaction paths of the HDS process,
were only vaguely guessed based on macroscopic evidences.

Copyright 2008 Oxford University Press

28 Chen: Introduction to Scanning Tunneling Microscopy

A systematic study of the structure, active sites, and reaction paths

is carried out with STM experiments and DFT computations [18]. In the
industry, MgAl2 O4 is usually used as substrates for the MoS2 clusters. How-
ever, it is not appropriate for STM studies because it is an insulator. For
STM studies, single crystal gold is chosen as the substrate, especilly the
Au(111) surface. Gold is relatively inert and allows for investigation of the
intrinsic properties of the catalysts.
The nanoclusters of MoS2 were prepared by depositing molybdenum on
Au(111) surface in an atmosphere of H2 S at a pressure of 1×10−6 mbar, then
the substrate was annealed to 673–723K for 15 minutes. A fairly uniform
distribution of crystalline MoS2 nanoclusters was formed. Most of the MoS2
nanoclusters appear to have a triangular shape, with an average area of 5
nm2 . The side length of each triangular nanocluster is about 3 nm. From a
combination of STM experiments and first-principles computations, it was
concluded that the edges are saturated with sulfur atoms [18].
By exposing the MoS2 nanoclusters with various substances, the reac-
tivity of MoS2 is studied with STM. It was found that MoS2 neither reacts
with organic molecules containing sulfur, such as alkanethiol (Cn H2n+1 SH)

Fig. 1.5. Reaction of H and thiophene with a MoS2 nanocluster. (a) The
triangular MoS2 nanocluster, after exposed to atomic hydrogen and then thiophene at
elevated temperature, is cooled down and characterized by STM. Image size: 5×5 nm2 .
Bean-like structures, identified as the intermediate product of thiophene, cis-but-2-ene-
thiolate (CH3 -CH=CH-CH2 -S− ), are found on the bright rim. Also, there is a prominent
change in the outermost rim protrusions, identified as sulfur vacancies. Part of the rim
is highlighted in (b). Details of a line scan of the rim is shown in (c). Solid curve (I):
STM line scan along the dashed line in (b). Dashed curve (II): the line scan of the
correspondent unreacted area, shown for comparison. (Original high-resolution image in
black-and-white by courtesy of J. V. Lauritsen. See [14, 18] for details.)

Copyright 2008 Oxford University Press

 Chen: Introduction to Scanning Tunneling Microscopy 29

and thiophene (C4 H4 S), nor reacts with H2 . Only after exposing MoS2
with predissociated (atomic) hydrogen, visible changes are observed. Sulfur
vacancies are created at the rims.
By further exposing the MoS2 nanoclusters already treated with atomic
hydrogen with thiophene (C4 H4 S), a strong reaction is found, as shown in
Fig. 1.5. As shown, parts of the rim are significantly altered. The outermost
protrusions of the rims are markedly shifted, and bean-like structures appear
adjacent to the bright rim.
The STM study revealed the mechanism of catalytic reaction. First, a
hydrogen atom reacts with the rim of a MoS2 nanocluster, strip off a sulfur
atom and expose a molybdenum atom. The molybdenum atom becomes
an active site. A alkanethiol molecule can chemically adsorb on the active
site by forming a S-Mo bond. After picking up a H atom, the hydrocarbon
molecule becomes free, and the sulfur atom occupies the S vacancy at the
rim of the MoS2 nanocluster. The desulphurization of thiophene is more
complex. At an active site of MoS2 , it is first converted to an intermediate
product, cis-but-2-ene-thiolate (CH3 -CH=CH-CH2 -S− ), and adsorbs on the
bright rim. Then it reacts further with hydrogen to become H2 S and alkenes.
The detailed understanding of the catalytic reaction at the atomic level
has resulted in improvements of the hydrodesulphurization catalyst.

1.5.2 Atomic-scale imaging at the liquid-solid interface

The atomic-scale phenomena at the liquid-solid interface is of significant sci-
entific and technological interest. Electrochemistry, and the related chemi-
cal industry, is based on atomic-scale reactions at the liquid-solid interface.
Most of the biological objects are only active in aqueous buffer solutions.
However, the traditional method for characterizing the surface relies on
ultra high vacuum, which cannot access the liquid-solid interface. The in-
vention of STM and AFM opened a wide window to study the atomic-scale
phenomena at the liquid-solid interface. Experiments showed that if the
liquid is clean, atomic resolution can be readily achieved. Furthermore, the
well-established methods of electrochemistry can be applied to change the
surface and the adsorbed atoms and molecules.
The pioneering works in this field [19, 20] showed a great potential of
operating STM in liquids by using a two-electrode system: the substrate
and the STM tip. Later on, by combining STM with the standard methods
of electrochemistry [21, 22], a four-electrode system was introduced [23, 24],
which provides a powerful, general and convenient method to study the
liquid-solid interface and a large number of electrochemical processes down
to atomic level.
Figure 1.6 is a schematic of STM in an electrochemistry cell. The stan-
dard electrochemistry cell contains three electrodes [25]. The working elec-
trode (WE) is the substrate under investigation. The reference electrode

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30 Chen: Introduction to Scanning Tunneling Microscopy

Fig. 1.6. The four-electrode electrochemical cell with STM. The standard elec-
trochemical cell has three electrodes: the working electrode (WE), the reference electrode
(RE), and the counter electrode (CE). By ramping the potential of the working electrode
back and forth, a cyclic current-potential curve can be generated. The STM tip is the
fourth electrode, to provide tunneling with the working electrode. To prevent the harm-
ful effect of oxygen, the entire cell is placed in argon atmosphere. (Original figure by
courtesy of J. Ulstrup’s group of Technical University of Denmark. See [26] for details.)

(RE) provides the reference potential, with insignificant electrical current

flow. Typically, a saturated calomel electrode (SCE) is used as the ref-
erence electrode [25]. The counter electrode (CE) supports the Faradaic
current to or from the working electrode. A routine experiment in electro-
chemistry consists of a cycle to ramp the potential of the working electrode
up and down with regard to the reference electrode. The Faradaic current
is recorded as a function of time, thus also a function of potential. The
cyclic current-potential curve, the so-called cyclic voltammogram, contains
a rich body of information regarding the electrochemistry at the liquid-solid
interface.
For STM experiments, a fourth electrode, the STM tip, is introduced.
The tip should be covered with an insulating film except on the very end of
the tip. The technique of making such a tip is described in Section 13.6.
Oxygen often reacts with the adsorbates of interest, especially biological
molecules. To improve the cleanness of the liquid-solid interface, oxygen
should be removed from the electrolyte. An effective method is to enclose
the entire system in an inert-gas atmosphere, such as nitrogen or argon. To
reduce the vibration caused by the flow of inert gas, a buffer bottle and two
valves are installed to limit the flow rate, see Fig 1.6.
As in all STM-related experiments, an important issue is to start with
an atomically flat, well-defined and well-understood substrate surface. The
Au(111) surface is an excellent substrate for the operation of STM in liquid.
Small pieces of single crystal gold can be generated by flame annealing
using a H2 flame. The single crystal, typically a few mm in diameter, shows
different crystallographic planes on its surface. After identified, a small piece
of gold chip is cut off from the sphere then mounted on a sample holder.
Au(111) samples can also be made by vacuum depositing gold on mica,

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 Chen: Introduction to Scanning Tunneling Microscopy 31

Fig. 1.7.
√ Au(111) surface imaged by STM in liquids. (a) At relatively large scale,
the 22× 3 reconstruction should be observed readily. (b) At smaller scale, individual
atoms should be observed. It provides a calibration of the x, y scales. (Original images
by courtesy of J. Ulstrup’s group of Technical University of Denmark.)

followed by annealing. The advantage of gold is that it does not oxidize in

air, thus the samples can √ be transferred through air. If the STM system
works properly, the 22× 3 reconstruction should be observed readily, see
Fig. 1.7(a). This provides a natural calibration for the x, y scales, and
the identification of the crystallographic orientations of the gold surface
with regard to the scan directions. If the tip is in good condition, atomic
resolution is achievable, see Fig. 1.7(b).
In the UHV environment, in order to change the surface reconstruc-
tion, depositing or removing a layer of atoms or molecules at the surface,
time-consuming and often irreversible annealing and vacuum evaporation
processes are required. In an electrochemical cell, those processes could
be accomplished within seconds by simply changing the potential, and are
almost always reversible. For example, the potential-induced reconstruc-
tion has been observed on all three low-Miller-index gold surfaces. In 0.1M
H2 SO4 , for potential Us <0.73 V, there is no stable SO2−4 adlayer. For po-
tential Us >0.73 V, a full ordered adlayer of SO2−4 is formed. Figure 1.8(a)
shows a voltammogram of the Au surface in 0.1M H2 SO4 .√The first peak at
about 0.35 V corresponds to the transition from the 22× 3 reconstruction
to the Au(111)-1×1 structure. The second peak around 0.73 V corresponds
to the formation of an ordered adlayer of sulfate. The very narrow peak
means that the ordered adlayer is formed within a very small potential
range. Figure 1.8(b) is an STM image of the Au(111) surface, recorded at
different potentials. The upper half, recorded at a potential of 0.65 V, shows
atomic resolution of the Au(111)-1×1 surface. The lower half, recorded at
a potential of 0.8 V, shows an ordered adlayer of sulfate.
In order to observe large biomolecules such as nucleotides and proteins
with STM or AFM in aqueous solutions, a key step is immobilization: to
adsorb the molecule on a flat surface without changing its functions. A

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32 Chen: Introduction to Scanning Tunneling Microscopy

Fig. 1.8. A voltammogram and an STM image of Au in 0.1M H2 SO4 . (a)

A voltammogram
√ of Au in 0.1M H2 SO4 . It starts at -0.35 V with a freshly prepared
Au(111)-22× 3 reconstruction.
√ The broad peak at 0.35 V signals the transition from
the Au(111)-22× 3 reconstruction to a 1×1 structure. The very sharp peak at around
0.73 V corresponds to the formation of an ordered adlayer of sulfate. (b) An STM image
of the Au(111) surface, taken at 0.65 V first, then changed the potential to 0.8 V. An
order adlayer of sulfate is formed. (Adapted with permission from Kolb [24]. Copyright
Wiley-VCH Verlag GmbH & Co. KGaA.)

commonly used method is to start with self-assembled monolayers of thiols

on atomically flat gold surfaces, for example, Au(111). The thiols, the or-
ganic molecules with a thiol functional group -SH, can form a strong S-Au
bond on gold surfaces (about 1 eV), leading to self-assembled monolayers.
The other functional groups in that molecule, such as -OH, -CH3 , -CHO,
could provide immobilizing anchors to the molecules of interest. Alkanethi-
ols Cn H2n+1 SH are the most commonly used thiols to form self-assembled
monolayers. Organic molecules containing carboxyl (-COOH) and amine
(-NH2 ) functional groups are important for immobilization of biological
macromolecules. Among the thiols, cysteine is of particular interest [27].
Cysteine (HS-CH2 -CHNH2 -COOH) is one of the 20 amino acids in pro-
teins, an indispensable building block of biological systems. Cysteine is a
particularly important building block in the formation of human hair, fin-
gernails, skin, and wool, and a ligand in many metalloproteins. Cysteine is
one of the two amino acids which contain sulfur, and the only amino acid
which contains a thiol group. A self-assembled monolayer of cysteine on
gold surface provides both the carboxyl group and the amine group for the
immobilization of biological macromolecules, especially proteins.
Self-assembled monolayers of cysteine are formed by exposing Au(111)
to a dilute solution of cysteine in 50 mM aqueous buffer electrolyte of am-
monium acetate (CH3 COONH4 ) [27]. The advantage of using ammonium
acetate is that pH is around 4.6, is mild to biomolecules, and it does not
adsorb on Au(111) surface over a quite wide potential range. A cysteine
concentration of 1 × 10−6 M is sufficient to build a highly ordered cysteine
monolayer under potential control. A gradual disappearance of the herring-

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 Chen: Introduction to Scanning Tunneling Microscopy 33

Fig. 1.9. Self-assembled monolayer of cysteine on Au(111). (a) A STM image of

the self-assembled monolayer of cysteine on Au(111). (b) Proposed model of its structure.
The sulfur atom is bonded to the Au(111) surface at the hollow site. (c) A ball-and-
stick model of cysteine. (Original figure by courtesy of J. Ulstrup’s group of Technical
University of Denmark. Reproduced with permission [27]. Copyright 2000 American
Chemical Society.)

bone pattern of the STM image signifies its formation.

A typical STM image of a highly ordered monolayer of cysteine thus
obtained is shown in Fig. 1.9(a). A structural model derived from the
experiments is shown in Fig. 1.9(b). A ball-and-stick model of cysteine is
shown in Fig. 1.9(c). As shown, the sulfur atom is bonded to a hollow site
of the Au(111) surface. The lateral interactions of cysteine finally generates
an ordered pattern.

1.5.3 Atom manipulation

In the speech entitled There’s Plenty of Room at the Bottom: An Invitation
to Enter a New Field of Physics [1], Richard Feynman posed a question
“Why cannot we write the entire 24 volumes of the Encyclopedia Britannica
on the head of a pin?” Such a dense writing requires that each dot of the
letters is 8 nm in diameter, a length of about 32 atoms in an ordinary metal.
In other words, each dot would contain in its area about 1,000 atoms. At
that time, such a dense writing was a fantasy.
The invention of STM has completely changed the scenario. Using STM
as a writing tool, features made of single atoms can be generated, far ex-
ceeded the goal of Feynman. With such a density, the publications of the
entire US Congress Library could be written on the head of a pin.
The basic operation of atom manipulation is to use the STM tip to
move an adatom from an initial position to a new position on a substrate,
as shown in Fig. 1.10. At the beginning, the atom for the designed structure
is deposited randomly on a substrate. Each atom is then an adatom on the
substrate at a random position. In order to move an adatom to another
stable location, an activation energy E must be applied to lift it across a
ridge to reach another stable position.
There are three steps for a move, see Fig. 1.10. Step A is to place the

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34 Chen: Introduction to Scanning Tunneling Microscopy

tip at the top of an adatom to be moved, then gradually increase the set
tunneling current. As a result, the tip moves towards the adatom. A partial
chemical bond is formed. When the chemical bond energy equals the barrier
energy, the tip should be able to pull the adatom over the ridge. Step B is
to move the tip sideways to pull the adatom to a desired location. Step C is
to gradually decrease the set tunneling current. As a result, the tip moves
away from the adatom and leaves it at the new position.
During the process of atom manipulation, neither the interaction energy
between the tip and the adatom nor the distance between the apex atom
of the tip and the adatom is known. The pioneers of atom manipulation
found from experience that this can be controlled by tunneling conductance,
or its inverse, the tunneling resistance. The threshold interaction energy
to allow the tip to pull the adatom over a diffusion barrier corresponds
to a threshold conductance, or equivalently, a threshold resistance [28, 29].
There is a general and fundamental relation between interaction energy and
tunneling conductance, which will be discussed in Chapter 5.
An example of the writing process is shown in Fig. 1.11. Those Chinese
characters were written using Ag atoms on Ag(111) surface using the above
process. At each stage of the manipulation, an image could be taken to
show the progress and to figure out the next steps to be executed. The
area of a complete Chinese character is 12 nm×12 nm. The size of each
dot is less than 0.8 nm×0.8 nm, 100 times smaller than that proposed by
Feynman.

Fig. 1.10. The basic steps of atom manipulation. First, position the tip to above
the adatom to be moved. Then, following the three steps: Step A, gradually increase the
set tunneling current to move the tip towards the adatom, until the interaction energy
between the tip and the adatom reaches the diffusion activation energy, the energy
required to move the adatom across the ridge between two adjacent stable positions. Step
B, pull the adatom to a desired location. Step C, gradually decrease the set tunneling
current to move the tip away from the adatom.

Copyright 2008 Oxford University Press

 Chen: Introduction to Scanning Tunneling Microscopy 35

Fig. 1.11. Writing Chinese characters using STM. A sequence of STM images
showing the assembly of two Chinese characters from single Ag atoms on a Ag(111)
surface. The lateral manipulation technique allows the exact placing of single atoms on
desired atomic sites. An assembly involves not only the movement of single atoms but
requires also many repair and cleaning steps until the final structure is completed [1].
(Courtesy of K.-F. Braun and N. Pertaya, Freie Universität Berlin.)

1.5.4 Imaging and manipulating DNA using AFM

In the same speech, There’s Plenty of Room at the Bottom [1], Richard
Feynman also proposed an approach for biology research using a microscope
capable of resolving individual atoms.

What are the most central and fundamental problems of biology

today? They are questions like: What is the sequence of bases
in the DNA (deoxyribonucleic acid )? What happens when you
have a mutation? How is the base order in the DNA connected
to the order of amino acids in the protein?...
It is very easy to answer many of these fundamental biological
questions; you just look at the thing! You will see the order of
bases in the chain; you will see the structure of the microsome.
Unfortunately, the present microscope sees at a scale which is
just a bit too crude. Make the microscope one hundred times
more powerful, and many problems of biology would be made
very much easier.

The invention of STM and AFM brings Feynman’s ultimate goal a lot
closer. Since the resolution of optical microscopy is limited by the wave-
length of light, which is a fraction of a micrometer, nearly atomic resolution

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36 Chen: Introduction to Scanning Tunneling Microscopy

is in principle impossible. The scanning electron microscope and the trans-

mission electron microscope can achieve a much better resolution. However,
the samples must be placed in a vacuum chamber, and often coated with
metal or other substances. At best those methods resemble a kind of au-
topsy. STM and AFM can, in principle, image live biological molecules,
and it is possible to image the process.
Because the biological molecules are poor conductors, AFM is more suit-
able. The AFM experiments are often performed in air or in an aqueous
buffer solution at room temperature. As long as proper sterilization is
carried out, clean environment could be achieved. Since the static-mode
AFM often damages the sample, tapping mode is frequently used. Com-
mercial AFM, such as Nanoscope IIIa, with commercial cantilevers and tips,
can be conveniently utilized. To date, true atomic resolution on biological
molecules is rarely achieved. Nevertheless, the nanometer-scale resolution
has already provided a lot of unprecedented first-hand microscopic informa-
tion on biological molecules. See Chapter 15 for details.

Immobilization and imaging

In order to use AFM to take images, the biological molecules must be immo-
bilized on an atomically flat surface without impairing its biological activity.
In Section 1.5.2, the method of immobilization for STM in an electrochemi-
cal environment is discussed. Gold surface with a self-assembled monolayer
of thiol derivatives is presented. For AFM, an insulating substrate works
equally well. One of the best substrates is silanated mica [30].
Mica can be easily cleaved to create atomically flat surfaces. However,
biomolecules do not adsorb on native mica surfaces. Treating mica with a
silanation agent, for example, 3-aminopropyl triethoxysilane (NH3 -(CH2 )3 -
Si-(O-C2 H5 )3 , usually abbreviated as APTS), dramatically improves adhe-
sion. Here, an ethyl group (-C2 H5 ) of APTS reacts with a hydroxyl group
(-OH) of mica, and then a strong Si-O-Si bond is formed. The amine group
(-NH2 ) is exposed and enables the adsorption of biomolecules.
Nevertheless, the bonding of DNA on APTS-treated mica is a little
too strong, thus the DNA molecules are often entangled. This situation
can be corrected using the method of “molecule combing”: by forcing
a fluid flow parallel to the surface, the DNA molecules are aligned to
the direction of the flow, thus effectively disentangled [31]. The original
method was demonstrated on glass surfaces. However, glass surface is not
flat enough for nanometer-scale AFM studies. By applying the molecule-
combing method to mica, under well-controlled conditions, very straight,
parallel DNA strands can be generated, as verified by AFM images [30].

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 Chen: Introduction to Scanning Tunneling Microscopy 37

Fig. 1.12. Manipulating DNA molecules using AFM. A pattern of DNA molecules
fabricated by AFM. First, DNA strands are deposited on an AP-mica surface. Second,
the AFM tip is positioned to a predefined location of the DNA strand, then pressed hard
to cut it. Third, the AFM tip is used to sweep or push the DNA strands to form a
designed pattern. (Reproduced from [32], with permission.)

DNA manipulation
The AFM has achieved beyond the target of Feynman: it is capable of not
only imaging, but also manipulating the biological molecules. Figure 1.12
shows an example of imaging and manipulating DNA molecules [32].
In those experiments, the DNA molecules are deposited on a mica sur-
face, pretreated with APTS for good adhesion. Those DNA strands are first
processed with a flowing buffer fluid, to form a more-or-less regular pattern.
Then, the AFM tip is used to manipulate the DNA strands to fabricate
designed patterns by the following sequence of actions.
The first action is molecular cutting. By positioning the tip at a pre-
determined location of the DNA strand, then pressing it hard, the DNA
strand could be broken at a point of nanometer accuracy.
The second action is sweeping or pushing. A fragment of a DNA strand
could be pushed by the side of the AFM tip, either to move it out of the
area of interest, or to reposition it to a predetermined location.
During the entire process, the DNA strands can be imaged with tapping
mode using the same AFM tip at any time. In Fig. 1.12, the DNA strands
are cut and pushed to create three letters: DNA.

DNA surgery
By combining the capability of AFM to manipulate the DNA with the
established methods in molecular biology, a procedure of DNA surgery was
demonstrated [33, 34]. Besides imaging, the AFM tip can dissect a DNA
molecule at designated positions, and then pick up a desired segment. The
tip, which holds the DNA segment, is transferred into a test tube. Using the
polymerase chain reaction process (PCR), invented by Kary Mullit [35], the
single DNA segment can be multiplied into billions of copies within a few
hours in a test tube with the help of an enzyme polymerase. For a rerview
of PCR, see Chapter 8 of [36]. The order of the nucleotide bases of the large

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38 Chen: Introduction to Scanning Tunneling Microscopy

Fig. 1.13. Cutting and picking up a DNA segment using AFM. (a) The original
DNA fragment. (b) The DNA fragment was cut at 150 nm and 450 nm locations. (c)
The DNA segment was missing in the subsequent images, after picked up by the AFM
tip. (Reproduced with permission from [34]. Copyright 2007 Institute of Physics.)

number of identical DNAs can be sequenced by the Sanger method. For a

review of the Sanger sequencing method, see Chapter 12 of [36].
The proof-of-concept experiment was performed with a relatively small
and well-understood DNA molecule, the linearized pRB322. It has 4362
base pairs (bp) and a theoretical length of 1483 nm. The experiment was
performed using Nanoscope IIIa in air at room temperature. The pBR322
DNA molecules were deposited on a APTS-pretreated mica substrate, then
straightened using the molecule-combing method.
Figure 1.13(a) shows an AFM image of the as deposited DNA molecule.
The DNA molecule was then dissected at two predetermined points to create
an isolated segment, see Fig. 1.13(b). By pushing the side of the tip against
that segment, it could adhere onto the tip. By imaging the substrate again
with AFM, it appeared the segment was missing, see Fig. 1.3(c).
To verify that the DNA segment was actually picked up by the AFM
tip, the tip was transferred into a sterile tube for a PCR process [35, 36].
The results of PCR were then investigated by Sanger sequencing. In the
very first set of experiments, among 20 attempts, 7 cases were positive: the
expected DNA segments were detected [33, 34].

Copyright 2008 Oxford University Press

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