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 AFMs 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)
||6 x 1 % (100)
||REQUIRED, no lab time until PL done to acceptable level
|IL, instrument lab reports
||3 x 4 % (400)
2 x 8 % (800)
1 x 12 % (1200)
|REQUIRED, missed lab = -2n % of final grade, where n is the
number of missed labs. Late reports
-1 pt/day, each lab report must be done to an acceptable
|EX, exams||2 x 10 %||REQUIRED, missed exam = -1n % of final grade, where n is the
number of missed exams
|PP/PA/PR, project proposal, abstract, presentation||1 %, 3 % (300), 4%||late work not accepted. PP and PA must be
done in order to participate in PR.
|CL, computer lab reports||7 x 2 % (200)||late work not accepted
|HW, homework||6 x 2 % (200)||late work not accepted||20
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
IL2: Acquiring an image
CL1: Image processing
ML1: Static spring constant
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
ML2: Tip imaging
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 15: Exam 1 on instrumentation
Class 10: Scanner calibration
IL4: Probe and scanner calibration
ML3: Dynamic spring constant
Unit 5, Force-curve mechanics
Class 11: Potentials, forces, and stiffnesses
Class 12: Force curves
Class 13: Mechanical properties
IL5: Acquiring and processing force curves
CL4: Potentials, forces, and stiffnesses
CL5: Surface forces and cantilever stiffness
ML4: Cantilever instabilities
ML5: Force curve of an infinitely stiff sample
Unit 6, Tip-sample interactions
Class 14: Surface forces
Class 16: Contact mechanics
Class 19: Molecular dynamics
IL6: Contact mechanics
CL6: Contact mechanics
CL7: Molecular dynamics
ML6: Force curve of an unknown sample
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
T or W in OH 009
|% This Week
|10 March 2012||Introduction
|Feedback and artifacts
|CL2. Feedback and
|IL3. Optimizing, LFM
|IL5. Force curves
|14 April||Patriot's Day,
|IL6. Contact mechanics
day, no class,
|21 April||Student talks
|If unavoidable, make-up labs
Unit 1, Fundamentals of
imaging (IWGN, IntroNST, IntroAFM, IL1, IL2, CL1, PG Chap.1&5;
SPMLab, UGI Chap.1-3)
1a. Define the
acronyms SPM, SXM, STM, AFM, SFM, LFM, and FFM.
1b. Know in which environments an SPM can operate.
1c. Sketch diagrams showing the difference between constant-height and constant-strength modes.
1d. State the advantages and disadvantages of AFM and the ways in which AFM can be used.
1e. Distinguish between the "top-down" and "bottom-up" approaches to nanotechnology.
1f. Know the effects of the basic image-processing options.
1g. Describe how to acquire and process a contact-mode constant-normal-force AFM image.
Unit 2, Difficulties of
imaging (PG Chap. 4, DraftSects2.2-3, IL3, CL2, CL3; UGI Chap. 4,
Unit 3, Other SPMs
modes (HLI, HLII, PG Ch.1, IL3, STM, FFM; UGII Chs.1&3,
Unit 4, Calibration
(DraftSect4.1, PG Chap.2, IL4, kc_Exercise; StiffCal, UGII Chap. 6)
Unit 5, Force-curve
mechanics (DraftChap5, IL5, CL4, CL5, FC_Exercise; MPM, UGII Chap. 4)
||Lab and homework materials
Things I've been showing you in class
Link to YouTube lessons, new as of D'13!
AFM.DRAFT, Draft of AFM book
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
IWGN, Nano brochure from IWGN
MDI, Molecular Dynamics I
MDII, Molecular Dynamics II
MPM, Mechanical Properties of Metals
PG, A Practical Guide to Scanning Probe Microscopy
SFA, Surface Forces and Adhesion
StiffCal, Stiffness calibration paper
StiffCalII, Another stiffness calibration paper
STM, Scanning Tunneling Microscopy
Computer Lab Instructions
Data Dlevers.pdf, Data sheet for stiff cantilevers
Data Grating, Data sheet for TGTcalibration grating
Data MPP31123, Data sheet for compliant cantilevers
EXP, Expectations of AFM Users
HW3, Homework 3
ICA, I.C.Adams manual *
ILI, Instrument Lab Instructions
ILR.docx, Template for Instrument Lab Reports (Word)
ILR.tex, Template for Instrument Lab Reports (LaTeX)
Lab5, Excel file for Lab 5 report
Lab6, Excel file for Lab 6 report
LP, Laboratory Procedures
MLI, Macro-Lab Instructions
ML1, Static spring-constant spreadsheet
No software for ML2
ML3, Dynamic spring-constant acquisition program
ML4, Cantilever-instabilities acquisition program
ML5&6, Force-curve acquisition program
SPMLab, Manual for V.5.01 *
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.
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.
will work individually on the computer labs and submit individual
lab reports. All lab reports and prelabs are to be on paper; electronic
versions will be accepted with a 20 % penalty. Instrument lab reports
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.
I will answer questions concerning the self-paced computer labs during our regularly scheduled sessions in SL 123 on Fridays at 12:00. If you miss a session, 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. You may also install it on up to two of your own computers, but you are not allowed to distribute it.
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 Rebecca L Gaddis, firstname.lastname@example.org, and Gawain Thomas, email@example.com.
You must pass EACH of the six instrument labs
in order to pass the course. If you have an important
or religious observance that conflicts with your regularly scheduled
session, you may switch lab times with a classmate, but you must inform
by email at least a day in advance. If unavoidable, lab make-ups will
held the last full week of the term. Missing an instrument lab
costs you 2n % of your final grade, where n is the number of missed
times. If you fail to comply
the laboratory procedures, you will not be permitted to use the lab;
you will not pass the course. If you were able to perform
lab work on time but your lab report is tardy, a one-point penalty per
day (out of twenty points) will be enacted. This does not stop at zero!
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
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
proposal, bring me hard copies of at least two related publications
you about modern materials, biophysics, or nanotechnology. At least one
must be from a 2010 or later peer-reviewed journal. (No web sites
unless they are web versions of hard-copy journals. A good place to
start is scholar.google.com.
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
or the New York Times. I want to ensure that the articles are
for your talk. (Are they related to the course? Are they specific
to summarize in a few minutes?)
see above for key-word links
|HW1, Fundamentals||1. Reading summary of IWGN, brochure introducing
nanoscience and technology
2. State in kilometers, microns, nanometers, Angstroms, and picometers how far it is from Olin Hall to where you live.
3. Estimate the magnitude of the pressure between a coffee cup and a desk. Write the result with the correct SI unit for pressure. Estimate the magnitude of the pressure between an AFM tip and a sample if the cantilever has a spring constant of 1 N/m, it is deflected by ten times the diameter of a hydrogen atom, and the contact area with the sample is a square nanometer. What is the SI prefix for this power of ten?
4. ML1, static spring constant.
|1. Reading summary of DraftSects2.2-3 on noise and FFTs
2. Problem 15, identifying noise
3. Problem 18, fourier coefficients
4. ML2, tip imaging
|HW3, Other SPMs
||1. Reading summary of DraftSect4.1 on probe design and
2. Problem 30, influence of thickness of cantilever
3. Scanner sketching exercise. Sketch the equivalent of Figs 2-5, 2-7, 2-10, and 2-11 in PG, not for a square step, but for a square well. There is a small mistake in Fig. 2-7. You should be able to puzzle out the mistake by comparing Figs. 2-6 and 2-7.
4. ML4, cantilever instabilities
|HW5, Force Curves
||1. Reading summary of DraftSects.5.1-2 on force-curve
2. Problem 45, instabilities for approach and retraction
3. Problem 55, taking limits
4. ML5, force curve of an infinitely stiff sample
||1. Reading summary of DraftSects.5.3 and 6.1 on materials
2. Problem 60, reduced modulus
3. Problem 68, forces and charges
4. ML6, force curve of an unknown sample
|PP, Presentation Proposal||Bring me hard copies of at least two related current publications that interest you about modern materials, biophysics, or nanotechnology. At least one article must be from a 2010 or later 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. A good place to start is scholar.google.com. 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. I want to ensure that the articles are appropriate for your talk. (Are they related to the course? Are they specific enough to summarize in a few minutes?)|
|PA, Presentation Abstract||The presentation abstract will reflect your understanding of the articles. It should be one page, at least 300 and fewer than 600 words in length, and submitted on paper at the beginning of class on the due date. Refer to the articles within the abstract.|
presentations, during which you will describe your articles in a short
verbal presentation, is contingent upon timely submissions of a
proposal and an abstract.
|DDD, Drop-Dead Day
||All IL and EX work must be submitted
before noon on 1 May 2013 in order to be included in your D-Term grade.