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Scanning tunneling microscopy and spectroscopy : I. Semimetals and semiconductors. II. Atom-resolved imaging of DNA


Driscoll, Robert James (1993) Scanning tunneling microscopy and spectroscopy : I. Semimetals and semiconductors. II. Atom-resolved imaging of DNA. Dissertation (Ph.D.), California Institute of Technology.


The topographic and electronic structure of semiconductor and semimetal surfaces were investigated using scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS), respectively. The longrange morphology and atomic-scale characteristics of cleaved materials such as highly oriented pyrolitic graphite (HOPG), boronated pyrolitic graphite (BPG), titanium disulfide, and gallium arsenide (GaAs) were revealed by STM performed under ultrahigh vacuum (UHV) conditions.

Atomic resolution constant-current and current-imaging data, as well as barrier height information obtained from tunneling gap modulation, are presented. Both point and line defects were observed on these surfaces; the origin and role of native and adsorbed surface defects are discussed. Visual evidence of coulombic screening caused by adsorption of charged species on n-type GaAs(110) is provided. The atomic corrugation of the GaAs surface was measured to be as little as 0.03 Å peak-to-valley, attesting to the stability of the microscope design. The BPG sample used in these studies consisted of up to 0.5% boron; boron is the only known substitutional impurity of graphite. Boron substituent atoms appeared as small protrusions approximately 3 Å in diameter, with an atom density consistent with the assumed concentration.The BPG surface exhibited frequent line defects, including large-angle grain boundaries, and monolayer-depth etch pits. Images of BPG in air using graphite tips showed similar results; the validity of the popular "sliding-planes" mechanism for graphite imaging is evaluated.

The effects of anisotropic stress on the morphology and reconstruction of a thermally annealed Si(111) wafer were explored. The height and orientation of step bunches, as well as terrace widths, on the (7x7) surface were determined. Electromigration effects were also observed; although the overall surface slope was conserved, the step bunches were "smeared out" by reversal of the current direction during heating. Line fault defects at step kinks were observed; a theory for the origin and structure of these features based on stress relief is proposed. Current imaging tunneling spectroscopy (CITS) and localized STS revealed differences between the adatom sites of the (7x7) surface. Atom-resolved barrier height images were also obtained;comparison to constant-current images may in fact provide a means of differentiating between defects and adsorbed species on the surface. The local effective barrier height was seen to depend strongly on the "cleanliness" of the STM tip. The barrier height increased dramatically following voltage pulsing on the order of ten volts. The large height of the step bunches also provided a good test to evaluate the sharpness of the STM tip; examples of "tip changes" affecting image resolution and "multiple-tipping" are provided. Silicon samples annealed at temperatures below 1000°C revealed substantial silicon carbide (SiC) contamination which effected step pinning. No SiC islands were observed on samples annealed above 1250°C.

In addition, atom-resolved STM images of duplex DNA supported on a HOPG surface were obtained in UHV. These images revealed double-helical structure, major and minor groove alternation, base pairs, and atomic-scale substructure. Comparison of the DNA dimensions derived from the STM data were in agreement with those from x-ray crystallography for "random-sequence" A-form DNA. Cross sectional profiles of the experimental STM data showed excellent correlation with the atomic contours of the van der Waals surface of A-DNA. Barrier height cross-sections showed general correlation with the atomic-scale topography over the phosphate-sugar backbone but distinct anticorrelation (complementarity) over the base pair region. The problems of aggregation and deposition coverage are discussed in the context of possible future applications of STM to DNA sequencing. The use of alternate techniques of DNA deposition, including electrospray ionization, for increased experimental reproducibility are described. The limitations of HOPG as a substrate for biomolecular adsorbates in STM experiments are evaluated.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Chemistry
Degree Grantor:California Institute of Technology
Division:Chemistry and Chemical Engineering
Major Option:Chemistry
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Baldeschwieler, John D.
Thesis Committee:
  • Unknown, Unknown
Defense Date:8 September 1992
Record Number:CaltechTHESIS:11292012-090633873
Persistent URL:
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:7294
Deposited By: Dan Anguka
Deposited On:29 Nov 2012 18:12
Last Modified:02 Dec 2020 02:12

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