MSE 6075: Nanoscale Probing and Imaging
co-listed as MSE 5050 (section 002), special topic for undergraduate


click to download the PDF of lecture notes

Lectures	Literature (to be upgraded throughout the semester)
Lecture 1: Introduction	Briefs of course, syllabus, handouts, and schedule, etc.
Lecture 2: Overview: Nanoscale Probing and Single-Molecule Imaging	http://www.nano.gov/ http://pubs.acs.org/cen/nanofocus/, World Future Society, 2007, January. Acct. Chem. Res., 1999, vol.32, p3888. Nano Lett, 2005, vol5, p2330. C&EN, 2000, issue of May 1, p41. Nature, 2000, vol408, p541. Science, 2003, vol301, p1882. Nature, 1998, vol391, p775.
Lecture 3: Traditional Microscopy Techniques	http://www.unl.edu/CMRAcfem/em.htm, Ann. Rev. Phys. Chem. 2004, vol.55, p159. Nature 2004, vol. 432, p36. Science 2003, vol.300, p1419.
Lecture 4: Review of Scanning Probe Microscopy (SPM)	http://en.wikipedia.org/wiki/Scanning_probe_microscopy and refs linked therein Phys. Rev. Lett. 1986, vol.56, p930. Chem. Rev. 2003, 103, p4367. Science, 1999, vol283, p661.
Lecture 5: Dip-Pen Lithography by SPM	Science,1999, vol.283, p661, Science,1999, vol.286, p523 Nature Chemistry, vol. 3, 2011, page 273-278 J. Am. Chem. Soc., 2001, vol. 123, p7887, J. Am. Chem. Soc., 2002, vol.124, p1560, Nano Lett, 2003, vol. 3, p757, Nano Lett, 2003, vol.3, p43, J. Am. Chem. Soc., 2003,vol. 125,p5588. Angew. Chem., Int. Ed. 2006, 45, 7220–7223. Nature Nanotechnology Volume: 5 , Pages: 637–640 (2010).
Lecture 6: Principles of Scanning Tunneling Microscopy (STM)	Chem. Rev., 1997, issue 4 (a special issue on STM), pp1015-1230. Science, 1997, vol. 275, 1097-1099. http://en.wikipedia.org/wiki/Scanning_tunneling_microscope and refs linked therein
STM Applications: Lectures 7-9
Lecture 7: Atomic Imaging of Metal and Semiconductor Surface	Phys. Rev. Lett. 1999, vol.83, p991. Science, 2000, vol. 287, p1474.
Lecture 8: Surface Mapping, Patterning, Manipulation of Atoms and Molecules	For Atoms: Phys. Rev. Lett. 1997, vol.79, p697, and 1996, vol. 77, p2133. Science, 1998, vol. 279, p542. Nature, 2000, vol. 406, p48. Science 2008, 319, p1066. For Molecules (Self-Assembly): Nature vol.425 2003, 602-605; Nature vol.424 2003,1029-1031; J. Am. Chem. Soc. 2006, 128, p4218.
Lecture 9: Single-Molecule Electronics via STM and Nanowire Junctions: Conductivity, Diode, Transistor	For Single Molecule Conductivity: Science, 2003, vol. 301, 1221-1223; Science, 2001, vol. 294, 571. Nano Lett, 2004, vol. 4, p267. J. Am. Chem. Soc. 2004, 126, p5370. Angew. Chem. Int. Ed. 2004, vol. 43, p6148. Also see the single-molecule junction based on nano-gap electrodes: Science, 1996, vol. 271, p1705. Science, 1997, vol. 278, p252. Phys. Rev. Lett. 2004, vol. 92, 188303-1;  J. Am. Chem. Soc. 2001, 123, 7730-7731; Appl. Phys. Lett, 2000, vol. 77, 3995-3997. For Single-molecule diodes and transistors: Nano Lett, 2004, vol. 4, p267. J. Am. Chem. Soc. 2005, 127, p2386. Nature, 2005, vol.435, p658. Science 2004, vol. 306, p2057. Appl. Phys. Lett, 2000, vol. 76, p3448. Science 2001, vol. 292, p706. Science 2001, vol. 291, p851. Nature, 2000, vol.407, p57. Nature, 2002, vol.417, p722. Nature, 2002, vol.417, p725. Nature, 2003, vol.425, p698. For Nanowire-junctions: Appl. Phys. Lett, 2001, vol. 78, p811. Science, 2003, vol. 301, 1221-1223; Phys. Rev. B 2003, vol. 68, p045302. C&EN, 2006, Feb. 13 issue, p45-51, and www.plasticlogic.com
Chemical Bonding and Reactions (Paper presentation) presentation dates TBD	Literature for reading: Nature, 2005, vol.434, p367. Science, 2007, vol. 315, p1391. Annu. Rev. Phys. Chem. 2003. vol54, p307, Phys. Rev. Lett. 2001, vol. 87, 166102-1. Phys. Rev. Lett. 2000, vol. 84, p1527. Phys. Rev. Lett. 2000, vol. 85, p2777.
Lecture 10: Basics of Atomic Force Microscopy (AFM) Different Feedback Modes of AFM	Rev. Sci. Instrum. 1994, vol.65, p2870. J. Biol. Chem. 2003, vol.278, p21655. http://en.wikipedia.org/wiki/Atomic_force_microscopy and refs linked therein
AFM Applications: Lectures 11-14
Lecture 11: Self-assembled nanostructures and nanomaterials	Science, 2002, vol 297, 72-75. Nature, 1998, vol 391, 775-778. Science, 2003, vol 301, 1882-1884; J . Mater. Chem., 2004, 14, 1959 – 1963. For Polymer materials: Angew. Chem. Int. Ed. 2002, vol41, 329-332; 1998, vol 37, p551.
Lecture 12: AFM measurement and imaging of chemical bonding	Science, 2001, vol 291, p2580. Science, 1994, vol 266, p771. J. Am. Chem. Soc. 2003, 125, p6725; J. Am. Chem. Soc. 2003, 125, p4560; Current Biology, 1999, vol.9, page R133-136.
Lecture 13: In vitro & In vivo Imaging of Proteins, Enzymes, and aggregates of small bio-species like peptides, particularly Amyloid Nanofibril Formation and relation to Alzheimer Disease.	J. Biol. Chem. 2003, vol.278, p21655. Proceedings of the National Academy of Sciences 2002, vol 99, 6725-30. J. Molecular biology, 1999, vol.285, p1347. For Amyloid Nanofibril: J. Biol. Chem. 2003, vol 278, 11612-22; 1999, vol 274, p32970-74.
Lecture 14: Imaging of DNA, Peptides and other small Bio-species: Genetic Recognition, Manipulation, self-assembly.	For DNA imaging: Nano Lett 2004, vol. 4, p1725. Nano Lett 2003, vol. 3, p39. J. Phys. Chem. B 2003, 107, p3591. More by Hao Yan at ASU.
Imaging Cell Membranes and Nano-surgery with AFM (Paper presentation) presem	Cell. Biology Inter. 1997, vol. 21, p685. Biophys. J. 2003, vol.85, p2746. Nano Lett 2005, vol. 5, p27. Langmuir, 2000, vol 16, 2789-2796.
Lecture 15: Two Special Modes of AFM Imaging for Electrical and Magnetic Materials: Electrostatic Force Microscopy (EFM) and Magnetic Force Microscopy (MFM)	For EFM: J. Phys. Chem. B 2005, 109, p1834. J. Phys. Chem. B 2004, 108, p4696. For MFM: J. Magnetism and Magnetic Materials, 1999, vol. 193, p511.
Lecture 16: Near-Field Scanning Optical Microscopy (NSOM) Different Working Modes of NSOM (Tips and Feedback)	Chem. Rev. 1999, vol 99, 2891-2927. Nano Lett., 2011, 11 (2), pp 355–360 http://en.wikipedia.org/wiki/Near-field_scanning_optical_microscope and refs linked therein
NSOM Applications: Lectures 17-19
Lecture 17: Imaging Single Molecules	J. Am. Chem. Soc. 2004, 126, p16126. Science 1993, vol. 262, p1422. Nature, 1994, vol.369, p40. J. Phys. Chem. A 1999, 103, p11264. Acc. Chem. Res. 1996, vol.29, p598. Nature 1997, vol.385, p143. Science 1994, vol.265, p361. Science 1996, vol.272, p255. Science 1994, vol.265, p364. Nano Lett., Vol. 4, 2004, 2091-2097. The new Science paper by Binnig.
Lecture 18: Optoelectronic Thin Films and Devices (LEDs, Solar Cells): Probing Optical/electrical Properties vs. Morphology and Nanostrucuture	For thin films: Phys. Rev. Lett. 2003, vol. 90, p016107. J. Phys. Chem. B, 1999, 103, p10138. J. Phys. Chem. B 2000, 104, p6728. J. Am. Chem. Soc. 2003, 125, p536; Acc. Chem. Res. 2005, vol. 38, p137. Acc. Chem. Res. 1997, vol 30, 204-12. For LEDs and Solar Cells: Nano Lett., 2004, Vol. 4, p219. J. Am. Chem. Soc. 1997, 119, 10608-10619.
Lecture 19: Scanning Confocal Microscopy (SCM)	Rev. Sci. Instruments, 2003, vol. 74, p3597. http://en.wikipedia.org/wiki/Confocal_microscopy and refs linked therein
SCM Applications: Lectures 21-22
Lecture 20: Single-Molecule Spectroscopy: Molecular Probes and Nanocrystal Optoelectronics	For Molecules: Ann. Rev. Phys. Chem. 1998, Vol.49, 441-480. Ann. Rev. Phys. Chem. 2004, Vol. 55, p457. Acc. Chem. Res. 1996, vol 29, 598-606. Chem. Rev. 1999, vol 99, p2929. J. Phys. Chem. 2002, vol 106, 910-927. J. Am. Chem. Soc. 2002, 124, p10640. Phys. Rev. Lett. 2004, vol 93, p236404. J. Am. Chem. Soc. 126 (2004) 16126 -16133. Angew. Chem. Int. Ed. 2003, vol. 42, p4209. For Nanocrystals: Nature Biotechnology, 2004, vol. 22, p969. Phys. Rev. Lett. 1996, vol 77, p3873. J. Phys. Chem. B 1999, 103, p1826. Science, 1997, vol. 278, p2114. Nature, 1996, vol. 383, p802.
Lecture 21: Imaging Molecule Rotation and Diffusion: Revealing Protein Conformational Structure through FRET, monitoring virus diffusion and attacking at living cell.	For Molecule Rotation and Diffusion: Phys. Rev. Lett. 1996, vol 77, p3979. Proc. Natl. Acad. Sci. USA, 1996, Vol. 93, pp. 2926–2929. For Protein Conformational Structure: Proc. Natl. Acad. Sci. USA, 1996, Vol. 93, p. 6424. Proc. Natl. Acad. Sci. USA, 2000, Vol. 97, p. 5179. 2926–2929. J. Phys. Chem. 2000, vol 104, p3676. Nature Cell biol. 2000, vol. 2, p168. For single virus imaging: Proc. Natl. Acad. Sci. USA, 2003, vol 100, 9280-9285. Nature Structural Mol. Biol. 2004, vol. 11,p567. Biophys J. 2004, vol. 87, p2749.
Lecture 22: Course summary and open discussion of Nano perspectives
Proposal Presentations	Dates to be announced in class
final week (no class)