In The Name of Allah

Scanning Tunneling Microscope

Pooria Gill

Ph.D. of Nanobiotechnology

Faculty of Medicine

Mazandaran University of Medical sciences

P.Gill@mazums.ac.ir

Image from an STM

Iron atoms on the surface of Cu(111)

Microscopy

Optical Microscopy

Scanning Electron Microscopy

Scanning Probe Microscopy

Scanning Probe Microscope

Atomic Force Microscope (AFM)

Electrostatic Force Microscope (EFM)

Magnetic Force Microscope (MFM)

Scanning Tunneling Microscope (STM)

Near-field Scanning Optical Microscope (SNOM)

History

The scanning tunneling microscope was developed at IBM Zürich in 1981 by Gerd Binning and Heinrich Rohrer who shared the Nobel Prize for physics in 1986 because of the microscope.

Gerd Binning Heinrich Rohrer

The STM is an electron microscope thatuses a single atom tip to attain atomic resolution.

Scanning Tunneling Microscope (STM)

SPM Systems

Piezoelectric Scanner

General Overview

An extremely fine conducting probe is heldabout an atom’s diameter from the sample.

Electrons tunnel between the surface and the tip,producing an electrical signal.

While it slowly scans across the surface,the tip is raised and lowered in order to keepthe signal constant and maintain the distance.

This enables it to follow even the smallestdetails of the surface it is scanning.

The Tip

As we will see later, is very important that thetip of the probe be a single atom.

Tungsten is commonly used because you can useElectro-chemical etching techniques to createvery sharp tips like the one above.

Quantum Tunneling

The second tip shown above is recessed by about two atoms and thus carries about a million times less current. That is why we want such a fine tip. If we can get a single atom at the tip, the vast majority of the current will run through it and thus give us atomic resolution.

Note

• A STM does not measure nuclear position directly.

• Rather it measures the electron density clouds on the

surface of the sample.

• In some cases, the electron clouds represent the atom

locations pretty well, but not always.

Converse Piezoelectricity

Piezoelectricity is the ability of certain crystals to produce a voltage when subjected to mechanical stress.When you apply an electric field to a piezoelectric crystal, the crystal distorts. This is known as converse piezoelectricity. The distortions of a piezo is usually on the order of micrometers, which is in the scale needed to keep the tip of the STM a couple Angstroms from the surface.

The tip

PizosElectric Field

Scanning Modes

STM Constant Current Mode

STM Constant Height Mode

System Components

Mechanical Parts

Electronics Parts

Computer + software

Needle replacementNeedle type

Platinum-iridium (PtIr)Tungsten tips Gold

Needle preparationElectrochemical etchingMechanical shearing

System Software Execution

Sample preparation

ZnO Nanoparticles around 6.5-8nm

Gold Nano crystals 6-14nm

Gold N

ano crystals 6-14nm

Gold Nano crystals 6-14nm

Calibration

Etching of atoms and molecules from the surface of gold (100x100nm) by our STM system

(a step for Nanorobotics)

Atomic resolution of graphite

4 ×4 × 0.2 nm

Atomic resolution of graphite

Advantages of Scanning Probe Microscopy

• The resolution of the microscopes • Create small structures nanolithography • Do not require a partial vacuum

Disadvantages of Scanning Probe Microscopy• The detailed shape of the scanning tip• Slower in acquiring images• The maximum image size

References

1. Pooria Gill, Bijan Ranjbar, Reza Saber. Scanning Tunneling Microscopy of Cauliflower-like DNA Nanostructures Synthesized by Loop-mediated Isothermal Amplification. IET Nanobiotechnology 2011; 5 (1), 8-13.

2. Reza Saber, Saeed Sarkar, Pooria Gill, Behzad Nazari, Faramarz Faridani. High Resolution Imaging of IgG and IgM Molecules by Scanning Tunneling Microscopy in Air Condition. Scientia Iranica (Transaction F: Nanotechnology) 2011; 18 (6), 1643–1646.

3. M.Q. Li. Scanning probemicroscopy (STM=AFM) and applications in biology, Appl. Phys. A 68, 255–258 (1999).

4. Errez Shapir et al., High-Resolution STM Imaging of Novel Single G4-DNA Molecules, J. Phys. Chem. B, Vol. 112, No. 31, 2008.

5. D. P. ALLISON. Immobilization of DNA for scanning probe microscopy, Proc. Nadl. Acad. Sci. USA, Vol. 89, pp. 10129-10133, November 1992.

6. Hiroyuki Tanaka. Visualization of the Detailed Structure of Plasmid DNA, J. Phys. Chem. B 16788 2008, 112, 16788–16792.

7. Hiroyuki Tanaka. High-resolution scanning tunneling microscopy imaging of DNA molecules on Cu(111) surfaces, Surface Science 432 (1999) L611–L616.

8. Handbook of microscopy for nanotechnology / edited by Nan Yao. Zhong Lin Wang. 2005 Kluwer Academic Publishers.

9. Scanning probe microscopes : applications in science and technology / K.S. Birdi. 2003 by CRC Press LLC.

10. SCANNING PROBE MICROSCOPY, 2007 Springer Science+Business Media, LLC.

Thanks for your Attentions

Mazandaran University of Medical Sciences and Health Care

Sari, I.R. Iran

www.mazums.ac.ir

STM: Applications in Biomedicine

Pooria Gill

PhD Of Nanobiotechnology

Faculty of Medicine

Mazandaran University of medical sciences

P.Gill@mazums.ac.ir

In The Name of Allah

Nanoscopy of Nanostructured Biomolecules

Structural Analyses

Interactiomics

Partial Sequencing

Immobilization Characterization

Peptide Characteristics

Microbial Characteristics

Viral Characteristics

…

Single strand of calf thymus DNA deposited along a surface step of HOPG. (50 x 50 nm, constant current mode, current 0.1 nA, bias voltage 500 mV.)

Methods In Molecular Biology, Vol 22. Microscopy, Opt/cat Spectroscopy, and Macmscop/c Technrqoes Edlted by: C Jones, I3 Mulloy, and A H. Thomas Copynght 01994 Humana Press Inc., Totowa, NJ.

STM of λ-DNA (GeneRuler DNA) on HOPG

P. Gill, B. Ranjbar, R. Saber. IET Nanobiotechnol., 2011, Vol. 5, Iss. 1, pp. 8–13.

3D image of a single antibody (IgG) molecule after the filtering and coloring process, which shows orientation of this molecule after physical adsorption on the rigid surface from the hinge region imaged by NAMA-STM

R. Saber, S. Sarkar, P. Gill, B. Nazari, F. Faridani. Scientia Iranica F (2011) 18 (6), 1643–1646.

3D image of a single antibody (IgM) molecule, imaged by NAMA-STM. (b) Standard configuration of human immunoglobulin M with pentameric domains

R. Saber, S. Sarkar, P. Gill, B. Nazari, F. Faridani. Scientia Iranica F (2011) 18 (6), 1643–1646.

STM

com

pa

rison

of

passiv

e

an

tibo

dy

ad

sorp

tion

an

d

bio

tinyla

ted

an

tibo

dy

linkag

e to

stre

pt

avid

in

on

m

icro

tite

r w

ells

STM

im

ages

of

antife

rritin

antib

odie

s passiv

ely

adso

rbed to

a

micro

well

surfa

ce

STM

im

ag

es o

f b

iotin

yla

ted

antife

rritin

an

tibo

die

s im

mob

ilized

to a

stre

pt

avid

in

coate

d

micro

well

surfa

ce

Davies et al., Journal of Immunological Methods, 167 (1994) 263-269.

Individual Peptide Structures Visible by STM

Reconstructed surface topography of coated T4 polybead capsomeres; (a) the TEM and (b) STM representations. The slight variation in the representation may be due to the overlying carbon film, which is observed by STM but not by TEM. Height range is 2.3 nm. (Reprinted with permission from Stemmer et al., 1989.)

M. FIRTEL and T. J. BEVERIDGE. Scanning Probe Microscopy in Microbiology. Micron, Vol. 26, No. 4, pp. 347-362, 1995.

Reconstructed surface topography of coated T4 polybead capsomeres; (a) the TEM and (b) STM representations. The slight variation in the representation may be due to the overlying carbon film, which is observed by STM but not by TEM. Height range is 2.3 nm. (Reprinted with permission from Stemmer et al., 1989.)

M. FIRTEL and T. J. BEVERIDGE. Scanning Probe Microscopy in Microbiology. Micron, Vol. 26, No. 4, pp. 347-362, 1995.

STM image of coated (a) sheath and (b) hoops from M. hungatei. Bars: x, y = 100 nm; z = 8 nm.

M. FIRTEL and T. J. BEVERIDGE. Scanning Probe Microscopy in Microbiology. Micron, Vol. 26, No. 4, pp. 347-362, 1995.

Thanks for your Attentions

Mazandaran University of Medical Sciences and Health Care

Sari, I.R. Iran

www.mazums.ac.ir