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Atomic force microscopes (AFMs) are instruments that allow three-dimensional imaging of surfaces with nanometer resolution. Also used to determine chemical and mechanical properties of surfaces, they and their cousins, collectively called scanning probe microscopes, are the principal enabling technologies in the fields of nanoscience and engineering. Nanoscience and engineering encompass many different disciplines, e.g. physics, chemistry, materials science, electrical engineering, and biology. Their common thread is the mutual focus on understanding, designing, and controlling processes and devices at the nanoscale.
If you complete this course, you will understand the functional principles of AFMs, be able to run one, and interpret the data that you collect. The course has two main parts. The first half of the term emphasizes instrumentation, the second half interpretation. Each week, there are three one-hour lectures, one one-hour computer lab, and one two-hour instrument lab. Successful completion of PH 1110 and 1120 are strongly recommended. PH 1130 and 1140 are also suggested. Previous students have indicated that the course was not only helpful to their research, but also in finding employment and securing admission to graduate school. You must pass the course in order to use the AFM in your future research. Auditors are welcome to sit in the lectures. However, they may not partake in the labs due to the high cost of supplies, the limited number of TAs, and licensing issues.
AFM | Grading
| Syllabus | Calendar
| Objectives | Materials
| Prelabs and labs | HW and
presentation | Communication and dates
| Type of Assignment |
# x % (Min.Words) |
Comments |
Pts. |
| PL, prelabs |
6 x 1 % (100) |
REQUIRED, no lab time until PL done to acceptable level |
5 |
| IL, instrument lab reports |
3 x 4 % (400) 2 x 8 % (800) 1 x 12 % (1200) |
REQUIRED, missed lab = -3.0 % of final grade, late reports
-1 pt/day (before 16:00), each lab report must be done to an acceptable
level |
20 |
| EX, exams | 2 x 10 % | REQUIRED, missed exam = -1.5 % of final grade | 50 |
| PP/PA/PR, project proposal, abstract, presentation | 1 %, 3 % (250), 6% | late work not accepted | 5 |
| HW, homework | 4 x 2.00 % | late work not accepted |
5/prob |
| CL, computer lab reports | 7 x 1.43 % (200) | late work not accepted |
5 |
| RS, reading summaries | 6 x 1.00 % (300) | late work not accepted | 10 |
| Rating | 5-pt scale |
20-pt
scale |
| acceptable |
3 |
11, 12 |
| good |
4 |
13, 14 |
| very good |
5 |
15, 16 |
| excellent |
- |
17, 18 |
| masterful |
- |
19, 20 |
| Approach: |
global |
itemized |
PART I – INSTRUMENTATION
Unit 1, Fundamentals of imaging
PART II – INTERPRETATIONClass 1: IntroductionUnit 2, Difficulties of imaging
Class 2: SPM and AFM instrumentation
IL1: Laboratory procedures
CL1: Image processing
IL2: Acquiring an image
Class 3: Feedback and artifactsUnit 3, Other SPMs and operational modes
Class 4: Perturbations and noise
Class 5: Fast fourier transforms
IL3: Optimizing an image and lateral force microscopy
CL2: Feedback and noise
CL3: Fast fourier transforms
Class 6: Scanning tunneling microscopyUnit 4, Calibration
Class 7: Lateral force microscopy
Class 8: Operational modes
IL3: Optimizing an image and lateral force microscopy
Class 9: Probe calibrationClass 13: Exam 1 on instrumentation
Class 10: Scanner calibration
IL4: Probe and scanner calibration
Unit 5, Force-curve mechanics
Class 11: Potentials, forces, and stiffnesses
Class 12: Force curves
IL5: Acquiring and processing force curves
CL4: Potentials, forces, and stiffnesses
CL5: Compliance
Unit 6, Tip-sample interactions
Class 14: Surface forces
Class 15: Basic mechanical properties
Class 16: Contact mechanics
Class 19: Energy dissipation and molecular dynamics
IL6: Contact mechanics
CL6: Contact mechanics
CL7: Molecular dynamics
Unit 7, A glimpse at current researchClass 17: Student presentations on current researchClass 20: Review
Class 18: Student presentations on current research
Class 21: Exam 2 on interpretation
| Week of | Monday | Tuesday | Instrument
Lab Tues or Weds in OH 009 |
Thursday | Computer
Lab Fridays in HL230 |
% this Week |
| 14 March 2010 | Introduction -- |
Instrumentation -- |
IL1.
Laboratory procedures PL1 |
Feedback and artifacts RS1 |
CL1.
Image processing -- |
1.6 %
|
| 21 March |
Perturbations and
noise RS2 |
FFTs IL1 |
IL2. Acquiring PL2 |
STM HW1 |
CL2. Feedback and
noise CL1 |
8.0 %
|
| 28 March | LFM RS3 |
Other modes IL2 |
IL3. Optimizing, LFM PL3 |
Probe calibration PP |
CL3.
FFTs CL2 |
8.0 %
|
| 4 April |
Scanner calibration RS4 |
UFk IL3 |
IL4. Calibration PL4 |
Force curves HW2 |
CL4. UFk CL3 |
8.0 %
|
| 11 April | Surface forces RS5 |
EX1, IL4 | IL5. Force curves PL5 |
Mechanical properties PA |
CL5. Stiffness CL4 |
26.7 %
|
| 18 April | Patriot's Day, no class -- |
Contact mechanics IL5 |
IL6. Contact mechanics PL6 |
Project presentation
day, no class, HW3 |
CL6. Contact
mechanics CL5 |
13.7 %
|
| 25 April | Student talks PR |
Student talks
PR |
If unavoidable, make-up labs, due on
Tuesday. RS6 |
Molecular dynamics IL6 |
CL7.
Molecular dynamics CL6 |
17.3 %
|
| 2 Mayl |
Review HW4 |
EX2
CL7 |
DDD | |
17.3 %
|
Unit 1, Fundamentals of imaging
1a. Describe the differences
among SPM, SXM, STM, AFM, SFM, LFM, and FFM. (PG Sects.1.0,
1.1)
1b. Know in which environments
an SPM can operate. (PG Sect.1.7)
1c. Sketch diagrams showing the
difference between constant-height and constant-strength modes. (PG
Sects.1.0, 1.1)
1d. State the advantages and disadvantages of AFM and the ways in
which AFM can be used. (IntroAFM)
1e. Distinguish between the "top-down" and "bottom-up" approaches
to nanotechnology. (IntroNST)
1f. Know the effects of the basic
image-processing options. (SPMLab, CL1)
1g. Describe how to acquire and process a
contact-mode
constant-normal-force AFM image. (PG Chap.5, UGI Chaps.
1-3, IL1, IL2)
Unit 2, Difficulties of imaging
2a. Describe how a feedback
circuit
works and how you can control it. (UGI
Chap.4, FB, CL2)
2b. Know how to optimize an image.
(UGI Chap.4, IL3)
2c. Know how to test for artifacts. (PG
Chap.4, UGI Chap.4)
2d. Identify common artifacts and be
able to rectify them. (PG Chap.4, UGI
Chap.4)
2e. Identify the four most important
types of noise and specify their characteristics. (DraftSect2.2,
CL2
)
2f. Know how SPMs are built, situated,
and protected so
as to limit perturbations. (DraftSect.2.2)
2g. Explain the principles of fourier theory and fourier
threshold filtering. (DraftSect2.2, CL3)
2h. Be able to improve
SPM images using fourier threshold filtering. (CL3)
Unit 3, Other SPMs and
operational
modes
Unit 4, Calibration
Unit 5, Force-curve mechanics
5a. Calculate all the
relationships
among potentials,
forces, and concavity. (DraftSect4.1, CL4)
5b. Understand the origins of cantilever
instabilities. (DraftSect4.1, CL5)
5c. Understand why and how raw force-curve data is converted
into processed data. (DraftSect4.1)
5d. List the advantages and disadvantages of weak and
stiff cantilevers. (DraftSect4.1)
Unit 6, Tip-sample interactions
Unit 7, A glimpse at current research
7a. Give some examples of current
research topics. (student presentations)
7b. Know how SPMs have contributed
to this research. (student presentations)
| Reading materials |
Lab materials |
| DraftSect2.2,
Combating Unwanted Perturbations DraftSect4.1, Force Curves FB, Feedback System Response in a Scanning Tunneling Microscope FFM, Friction Force Microscopy HLI, Looking at Atoms HLII, Stroking Molecules IntroAFM, Poster introducing AFM IntroNST, Poster introducing nanoscience and technology MPM, Mechanical Properties of Metals PG, A Practical Guide to Scanning Probe Microscopy SFA, Surface Forces and Adhesion StiffCal, Stiffness calibration paper STM, Scanning Tunneling Microscopy |
CLI,
Computer Lab Instructions Data Dlevers.pdf, Data sheet for stiff cantilevers Data gratings, Data sheet for calibration gratings Data Ultralevers.pdf, Data sheet for compliant cantilevers EXP, Expectations of AFM Users ICA, I.C.Adams manual * ILI, Instrument Lab Instructions ILR, Template for Instrument Lab Reports Lab5, Excel file for Lab 5 report Lab6, Excel file for Lab 6 report LP, Laboratory Procedures SPMLab, Image Analysis Menu Items (Chaps 4-6) * UGI, User's Guide for the M5 Instrument, Part I (Chaps 1-4) * UGII, User's Guide for the M5 Instrument, Part II (Chapter 4) * * The asterix indicates that the document is long and might not be worth printing. |
Between lab reports and prelabs, labs are worth 60 % of your final grade. You will work in teams of two on the instrument, but you will submit individual instrument lab reports. You will work individually on the computer labs and submit individual computer lab reports. All lab reports and prelabs are to be on paper; electronic versions will be accepted with a 20 % penalty. Instrument lab reports should use the template provided in the Study Materials section, and figures should be on separate sheets of paper, stapled to the back of the reports. Find out what to do in the Computer Lab Instructions and Instrument Lab Instructions respectively. Click here for the Instrument Lab Schedule .
I will answer
questions concerning
the self-paced computer labs during our regularly scheduled sessions in
HL
230 on Fridays at 12:00. If you miss a session, no help will be given
to
you and your lab report will be expected to be of the same quality as
if
you had attended. It is also due at the regularly scheduled time. No
late
reports will be accepted. Any of the almost four-hundred public
computers on campus offers the course software.
The first three instrument labs are for you to learn how to take a good image and are each worth 4 % of your final grade. The fourth concerns calibration, the fifth how to acquire and process a force curve. These are each worth 8 % of your final grade. After learning the basics in the first five labs, the capstone experience is the experiment in the sixth lab where you will take a high-quality image, then acquire and interpret a force curve after calibrating the probe's tip and spring constant. This last lab report is worth 12 % of your final grade. If you have a question about the labs as you write your reports, see me, or talk to the TAs. They are Ms Saonti Chakraborty, saonti@wpi.edu, OH 114, X-5758, and Mr Nihar Pradhan, nihar@wpi.edu, OH 004, X-5282. Ms Deli Liu, deli@wpi.edu, OH 220, X-5391, is my postdoc and can help you if you cannot find the regular TAs or me.
You must pass EACH of the six instrument labs
in order to pass the course. If you have an important
appointment
or religious observance that conflicts with your regularly scheduled
lab
session, you may switch lab times with a classmate, but you must inform
me
by email at least a day in advance. If unavoidable, lab make-ups will
be
held the last full week of the term. Missing an instrument lab
session
costs you 3 % of your final grade. If you fail to comply
with
the laboratory procedures, you will not be permitted to use the lab;
you will not pass the course. If you were able to perform
the
lab work on time but your lab report is tardy, a one-point penalty per
business
day (out of twenty points) will be enacted. This does not stop at zero!
If,
for example, you fail to turn in Lab 1 on time, and instead wait six
weeks before submitting it, it is worth at most minus ten points.
Instrument labs are
an essential part of the course, and this grading scheme reflects their
importance.
The presentation is a means for you to explore a subject that
interests you. You will synthesize at least two related articles
in cogent fashion for me and the rest of the class. For the
presentation
proposal, bring me hard copies of at least two related publications
that interest
you about modern materials, biophysics, or nanotechnology. At least one
article
must be from a 2000 or later peer-reviewed journal. (No web sites
unless they are web versions of hard-copy journals. A good place to
start is www.vjnano.org. Let us
define peer-reviewed journals as those
that appear in the Thomson
ISI master journal list , although this definition is more
convenient than accurate.)
The other may be from a popular science source, such as Discovery
Magazine
or the New York Times. I want to ensure that the articles are
appropriate
for you to talk. (Are they related to the course? Are they specific
enough
to summarize in a few minutes?)
The presentation abstract will reflect your understanding
of the articles. It should be at least 250 and fewer than 500 words in
length, using the same formatting as the abstract
in
the template for the instrument lab reports,
and submitted on paper at the beginning of class on the due date.
Refer to the articles within the abstract and staple the
articles to the back. The presentation is your verbal capsule thereof,
where
you will describe your articles in a short speech. You may also come to
the
blackboard or use the overhead projector.
| Homework | Assignment |
| HW1, Basic instrumentation | Syllabus; PG Intro; PG Sections 1.0,
1.1, 1.7; PG Chapter 5 |
| HW2, Nanoscience |
IntroAFM; IntroNST |
| HW3, Feedback and artifacts |
PG Chapter 4; UGI pp 4-11 to 4-15; FB |
| HW4, Perturbations and noise |
DraftSect2.2, Sections 2.2.1-2.2.2 |
| HW5, FFTs | DraftSect2.2, Section 2.2.3 |
| HW6, STM | HLI; STM |
| HW7, LFM |
HLII; FFM |
| HW8, Other modes | PG Sections 1.2-1.6 |
| HW9, Probe calibration |
PG Chapter 3;
StiffCal |
| HW10, Scanner calibration |
PG Chapter 2 |
| HW11, UFk |
DraftSect4.1, Sections 4.1.1-4.1.2 |
| HW12, Force curves |
DraftSect4.1, Sections 4.1.3-4.1.4 |
| HW13, Surface forces |
SFA Sections 3.0-3.6 |
| HW14, Mechanical properties |
MPM |
| HW15, Contact mechanics |
SFA Sections 4.0-4.2 |
| HW16, Molecular dynamics |
SFA Sections 4.3-5.2 |
| HW17, Review |
Send me two review
questions about the second half of the course. |
| PP, Presentation Proposal | Bring me hard copies of at least two related current (2000+) publications that interest you about modern materials, biophysics, or nanotechnology. At least one article must be from a peer-reviewed journal. The other may be from a popular science source, such as the New York Times or Discovery Magazine. If one article refers to the other, the two articles likely concern the same topic. For peer-reviewed journals, a good place to start is www.vjnano.org . Let us define peer-reviewed journals as those that appear in the Thomson ISI master journal list , although this definition is more convenient than accurate. |
| PA, Presentation Abstract | The presentation abstract will reflect your understanding of the articles. It should be at least 250 and fewer than 500 words in length, using the same formatting as the abstract in the template for the instrument lab reports, and submitted on paper at the beginning of class on the due date. Refer to the articles within the abstract and staple the articles to the back. |
| PR, Presentation | Be ready to describe your articles in a short verbal presentation. You may come to the blackboard or use the overhead projector. |
| DDD, Drop-Dead Day |
All IL and EX work must be submitted
before noon on 1 May 2008 in order to be included in your D-term grade. |