Course Syllabus

MSE 6075: Nanoscale Probing and Imaging

 

Instructor:

Dr. Ling Zang

Office:

Room 5543 SMBB building, 36 South Wasatch Dr.

Office Hours:

M&F, 12:00 pm �C 2:30 pm, or by separate appointments (email).

Phone:

587-1551

Email:

LZang@eng.utah.edu

Course web: http://www.eng.utah.edu/~lzang/teaching/mse6075.html

 

Teaching Assistant:

Yaqiong Zhang

Office:

Room 5520 SMBB building, 36 South Wasatch Dr.

T.A. Hours:

3:00 pm to 5:00 pm, Tue & Thur

Phone:

587-1547

Email:

yaqiong.zhangmse@gmail.com

 

Lecture:

MF 3:00 �C 4:20 pm, WEB 1450

Credit Hours:

3

 

Text(s):

No primary textbook required.

Necessary reading materials will be provided during class.

 

 

Course Description:

This course is designed to teach graduate students the basic principles of electronic microscopy and scanning probe microscopy and spectroscopy and their application in nanoscale probing and imaging, as well as single molecule detection.  It is designed for improving the understanding and interest in nanoscience and nanotechnology.

 

Content Overview:

The instructor, Prof. Ling Zang, will be lecturing the class and supervising the paper and proposal presentations (as scheduled) throughout the semester.  The students are expected to keep regular class attendance if ever possible to keep up with the lecture materials, and finish up the paper and proposal presentation and turn in the written proposal in time.  Both the two presentations are encouraged to be made in the format of PowerPoint.  Computer and projector will be provided as needed.  Working together, the instructor and students are expected to build up an interactive, dynamic classroom, where all students are involved in active discussion and challenging with questions --- learning through questioning.

Course Objectives for students:

  • to gain an understanding of the basic principles of electronic microscopies, scanning probe microscopies (AFM, STM, NSOM) and confocal microscopies;
  • to learn the broad application of the microscopy techniques in various research fields, crossing nanomaterials, nanotechnology and nanodevices;
  • to understand the principles and advantages of nanoscopic imaging, probing and spectroscopy, including single-molecule imaging;
  • to develop critical and creative thinking skills of using the microscopy techniques  to solve problems in 'real-world' research and materials engineering.

 

 

Grading & Evaluation Methods:

There is no exam in this course. The final grade will be based on class performance (including questioning, discussion, attendance etc.), paper presentation, and final proposal writing and presentation (see the table below for full grading distribution).

Throughout the semester, each student will be required to present one published paper before the class (20 min, plus 5 min for discussion) as if it were your work and be prepared for answering or defending related questions. The paper to be presented will be provided one week before the presentation. Each student will also be required to write a research proposal in "professional" format (~ 1500 words) and present it orally before the class in 20 min (plus 5 min for discussion). The guideline for writing the proposal is provided below. The deadline for turning in the written proposal is the last lecture before the proposal presentation week. Grading of the written proposal will be based on 100 points scale.  Turning in after the deadline will be considered as late work and points will be deducted for the late work: turn in one day late, 5 points deducted; two days late, 10 points deducted, and continue with 5 points deducted for each additional day late. 

The paper and proposal presentation will be given during the lecture times as scheduled. No makeup will be given for a missed presentation. If you have an unavoidable excuse for missing a presentation, the grading weight of that presentation will be transferred to the other grading categories as illustrated below in the grading distribution table. Valid excuse for missing a presentation includes critical health problems, critical family related issues or any other unexpected critical situations that make it unable to attend the class and finish up the presentation on time.

 

Grading Distribution

 

class performance

15%

paper

presentation

20%

proposal writing

40%

proposal presentation

25%

Grading Scale

(based on 100 points)

A

90-100

A-

80-89

B

65-79

C

50-64

D

35-49

F

< 35

 

 

Guideline for paper presentation:

  1. Present it as if it were your work.
  2. Presentation (in format of PowerPoint) should be within 20 min, plus 5 min for discussion and answering questions from the audience. 
  3. Presentation should cover not only the data and materials described in the paper, but also the related background and current stage of the specific research topic or field, aiming to provide the audience clear insight into the merit and significance of the reported work. 
  4. Don't accept by default that the reported experimental approach is the best to solve the raised problems.  If necessary, you may try to propose some new technical or specific microscopy improvement that may bring new or better results to the research, helping clarify the scientific argument.  Particularly some new technical improvements, regarding the microscopy imaging, are always available after the paper was published.
  5. The grading of the presentation will be a combined evaluation of the following aspects: presentation of novelty/significance/background of the topic subject, description and justification of the major experimental design, presentation of the important results and the discussion related to the main topics, the content of the presentation (organization, completeness, references, etc.), presenter's overall understanding of the research, and clearness of the presentation, and response to the questions. 


Guideline for proposal writing:

  1. Totally about ~ 1500 words, excluding the abstract (200-250 words) and the references.
  2. The proposal should be focused on a research topic, which is tightly associated with one or more scanning probe microscopy techniques; a good justification of why that specific microscopy technique is critical for solving the proposed problems.
  3. Pick a topic by yourself, but your are welcome to ask for suggestions.
  4. The proposal should consist of title, abstract, overview (background and significance), experimental designs and methods, major facilities (mainly the proposed microscopy technique along with other conventional instrumentations as needed), and references. 
  5. You should present clearly the objectives and scientific significance of the proposed work, the rationale for selecting the proposed experimental approach (particularly the microscopy imaging or probing techniques) to achieve the objectives.

Guideline for proposal presentation:

  1. Present it as described in the proposal, covering the major parts, including overview (background and significance), experimental designs and methods, major facilities, and references.
  2. Presentation (in format of PowerPoint) should be within 20 min, plus 5 min for discussion and answering questions from the audience. 


The grading of the presentation will be a combined evaluation of the following aspects: presentation of novelty/significance/background of the proposed topic, description and justification of the major experimental design and methods, presentation and discussion of the major outcomes and/or potential observations, the overall quality of the presentation regarding organization, clearness, completeness, as well as the response to the questions.

 

Key Dates:

Monday, September 1st - Labor Day - No School
Wednesday, September 3rd - Last day to drop classes
Monday, September 8th - Last day to add classes
Monday - Friday October 12th - 19th - Fall Break
Friday, October 24th - Last day to withdraw from classes
Thursday - Friday November 27th - 28th - Thanksgiving Break - No School
Friday, December 12th - Last day of classes

Final week, December 15-19

No Final Exam for MSE 6075.

 

Americans with Disabilities Act Statement:

"The University of Utah seeks to provide equal access to its programs, services and activities for people with disabilities. If you will need accommodation in the class, reasonable prior notice needs to be given to the Center for Disability Services, 162 Union Building, 581-5020 (V/TDD). CDS will work with you and the instructor to make arrangements for accommodations."

 

Faculty and Students�� Responsibilities:

"All students are expected to maintain professional behavior in the classroom setting, according to the Student Code, spelled out in the Student Handbook. Students have specific rights in the classroom as detailed in Article III of the Code. The Code also specifies proscribed conduct (Article XI) that involves cheating on tests, plagiarism, and/or collusion, as well as fraud, theft, etc. Students should read the Code carefully and know they are responsible for the content. According to Faculty Rules and Regulations, it is the faculty responsibility to enforce responsible classroom behaviors, and I will do so, beginning with verbal warnings and progressing to dismissal from class and a failing grade. Students have the right to appeal such action to the Student Behavior Committee."

 

Tentative Class Schedule:

click to download the PDF of lecture notes

Date

Lectures

Literatures (to be upgraded as lecturing)

8/25

Lecture 1: Introduction

Briefs of course, syllabus, handouts, and schedule, etc.

8/29

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.

9/5

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.

9/8

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.

9/12

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�C7223. Nature Nanotechnology Volume: 5 , Pages: 637�C640 (2010).

9/15

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

 

9/19

Lecture 7:

Atomic Imaging of Metal and Semiconductor Surface

Phys. Rev. Lett. 1999, vol.83, p991. Science, 2000, vol. 287, p1474. 

9/22

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.

9/26

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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

 

10/3

Chemical Bonding and Reactions

(Paper presentation)

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.

10/6

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

 

10/10

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 �C 1963.

For Polymer materials:
Angew. Chem. Int. Ed. 2002, vol41, 329-332; 1998, vol 37, p551.

10/20

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.

  

10/24

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.

10/27

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.

10/31

Imaging Cell Membranes and Nano-surgery with AFM

(Paper presentation)

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.

11/3

 

 

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.

11/7

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�C360

http://en.wikipedia.org/wiki/Near-field_scanning_optical_microscope and refs linked therein

    

NSOM Applications: Lectures 17-19

 

11/10

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.

11/14

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.

11/17

Lecture 19: (skipped due to LZ travel, but encouraged for self-learning from the literatures listed right side.  Some contents integrated into other lectures.)

Charge Transfer at Nanometer Interfaces: Impact to Real Optical/Electrical Devices and  a Special Application in Photolithography and Recording

For Nanoscale Interface Charge Transfer:

J. Phys. Chem. 1997, vol 101, p2753. i2002, vol 106, 910-927. Science 1991, vol. 251. p919.  Science 2001, vol. 291, p1519. 

 

For Nascale Photolithography and Recording:

Science 1999, vol.283, p661.   Nano Lett.  2004, vol. 4, p1381. Nano Lett., Vol. 4, 2004, 835-839.  Appl. Phys. Lett, 2003, vol. 82, p3313.

11/21

Mapping Membrane Proteins with NSOM

(Paper presentation)

Appl. Phys. Lett. 2003, vol.83, p5083.  FEBS Lett. 2004, vol. 573, p6. Biophysical Journal, 2004, vol.87, p3525. Proc. Natl. Acad. Sci. USA, 1997, Vol. 94, pp. 520�C525. Biophysical Journal, 1998, Vol. 74, p2184.

11/24

Lecture 20:

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

 

12/1

(to be combined with Lecture 22)

Lecture 21:

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.

12/5

 

Lecture 22:

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�C2929.

 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�C2929.  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.

12/5

 

12/8

12/12

 

Proposal Presentation

Proposal Presentation

Proposal Presentation

 

 

12/15-19

final week (no class)

 

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