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PH 561, Atomic Force Microscopy

Spring 2018
Prof NA Burnham, Physics Department
nab@wpi.edu , X-5365, OH 219

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. In general, each fortnight there are three one-hour lectures, one one-hour computer lab, and one two-hour instrument lab. A bachelor's degree in science or engineering is sufficient background. Previous students have indicated that the course was not only helpful to their research, but also in finding employment. You must pass the course in order to use my 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.

The course objectives are:

AFM | Grading | Calendar | Prelabs and labs | Other work | Writing Center | Communication and dates


Here is the grading scheme:
Type of Assignment
# x % (Min.Words)
PL, prelab quizzes
6 x 1 %
REQUIRED, no lab time until PLQ done to acceptable level

IL, instrument lab reports
3 x 3 % (300)
2 x 6 % (600)
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 level

EX, exams 2 x 10 % REQUIRED, missed exam = -1n % of final grade, where n is the number of missed exams
PP, LRP proposals
2 x 1 %
late work does not earn credit
PR, Project
1 x 3 %
late work not accepted
LR, abstract + talk
2 x 4 %
late work not accepted
ML, macro-lab reports
6 x 1 %
late work not accepted
CL, computer lab reports 7 x 2 % (200) late work not accepted
Q, quizzes at Canvas
16 x 0.5 %
late work not accepted 20

Here is how to interpret the grading scale:

Rating 5-pt scale
Suggests competence
Demonstrates competence
Suggests mastery
Demonstrates mastery

The grading is done globally, meaning that your grade depends on the overall quality of your work. Assignments shorter than the minimum word count will be returned ungraded.  Electronic submissions will suffer a 20 % grade penalty.  There are four aspects of the lab reports that are graded on the five-point scale; this accounts for the twenty-point total.  Similarly, there will be ten questions on each exam.

Only eight times this semester is your attendance essential –  the six instrument labs and the two exams. Attendance is not otherwise controlled, although be forewarned that there are topics that will be covered in class for which there is no available reading or notes. Important announcements are usually made at the beginning of class, so it is useful to be on time. If your final grade is near the border between two grades, e.g. between A and B, then your participation and enthusiasm will determine which grade you ultimately receive. The grading is structured such that if you do well on the instrument labs and exams, you still might pass the course if you neglect the computer labs, macrolabs, presentations, and homework. But it is unlikely that you will do well on the exams if you ignore such a large fraction of the work. I am not sympathetic to point grubbing, but I certainly would like to see blatant errors on the part of the graders (myself included). Nominally, 80 % or above is an A, 70 % or above B, and 60 % or above C. These lower borderlines for grades might initially seem encouraging. Yet I shall be most pleased if you come to think of me as a demanding grader. After the first exam, I shall give you an indication of how well you are doing.

The above is summarized by this calendar.

PL = PreLab, IL = Instrument Lab, CL = Computer Lab, ML = MacroLab, EX = Exam, PP, LRP = Proposals for your project and literature review. Bold indicates that the assignment is required and must be done to an acceptable level. Underlined means that the assignment is required. Italics show the six instrument labs and seven computer labs. The text colors distinguish among the seven units of the course. The pink backgrounds correspond to days that we do not meet for class.

Week of Monday
Week of
Instrument Lab
OH 114
% this

7 January Introduction
14 January MLK Day, no class CL1. Image processing
ML1, Static k
IL1. Lab procedures
3.0 %
21 January Feedback and artifacts
Q3, CL1
Noise and perturbations
ML2, Tip imaging
28 January
CL2. Feedback and noise
IL2.  Scan options
8.5 %
4 February CL3. FFTs
11 February LFM
Q7, IL2
Reading Day
No class but LAB

IL3. Optimizing
7.0 %
18 February Other modes
Q8, CL3
Probe calibration
Q9; ML3, Freq shift
25 February Scanner calibration
Q10, IL3
Q11; ML4, Dynamic k
IL4. Calibration
10.0 %
11 March Force curves
Q12, PP
CL4. UFk
ML5, Instabilities
18 March Mechanical properties
Q13, IL4
IL5. Force curves, project
20.0 %
25 March Surface forces
Q14, CL4
CL5. Stiffness
ML6, Unknown
1 April Contact mechanics
Q15, IL5
CL6. Contact mechanics
IL6. Capstone, project
13.0 %
8 April Molecular dynamics
Q16, CL6
CL7. Molecular dynamics
15 April
Patriot's Day, no class
IL6 due by noon Tuesday
Project talks
Complete project work
20.5 %
22 April Lit rev talks

Lit rev talks
29 April


Happy Summer!

18.0 %

Prelab quizzes and labs

The six prelab quizzes that are due at the beginning of your instrument labs are required before you may begin the lab. Find these assignments within the Instrument Lab Instructions. They must be done to an acceptable level. Each prelab quiz, graded out of five points, is worth 1 % of your final grade. The TAs have the right to penalize your prelab grade if you come to lab unprepared or if you are inattentive to laboratory procedures.

Between lab reports and prelabs, labs are worth 59 % of your final grade. You will work in teams of two or three 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. Macrolabs may be done in teams or individually, but the reports must be prepared individually.  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 at Canvas. Find out what to do in the Computer Lab Instructions, Macro Lab Instructions, and Instrument Lab Instructions respectively. 

I will answer questions concerning the self-paced computer labs during our regularly scheduled sessions. 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 3 % of your final grade. The fourth concerns calibration, the fifth how to acquire and process a force curve. These are each worth 6 % 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 one of the TAs.

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 2n % of your final grade, where n is the number of missed times. 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.

Other work:  Canvas quizzes, project, literature review

The course is run in "flipped" format, meaning that you are responsible for reviewing the lectures on YouTube prior to a class meeting.  In class we shall discuss any questions you might have and do worksheets together.  The worksheets are the basis for the exams.  In order to motivate you to review the lectures, there are short quizzes on Canvas. These are due by 8am on days when we are scheduled for a discussion.

The "nano" project is an opportunity for you to spend a lab session or two investigating a sample or two of your choosing.  You will give a three-minute presentation to the class near the end of the semester about your sample(s) and your data.  These data are to be collected by you individually during the second half of the semester, outside of our scheduled contact hours.  The proposal for it just requires that you speak to me before or on the first day after spring break -- I want to ensure that each student works on a different material.

The literature review is a means for you to explore a subject that interests you. You will synthesize at least six 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 that interest you about modern materials, biophysics, or nanotechnology. One article must be from a 2015 or later peer-reviewed journal. (No web sites unless they are web versions of hard-copy journals. 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.) One article may be older and from a popular science source, such as Discovery Magazine or the New York Times. 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? Is each student responsible for a different topic?)  You may bring me your proposals anytime after spring break.  I certainly want to see them by early April.

The abstract of the literature review will reflect your understanding of the articles. It should be one page, between 400 and 600 words in length, and submitted on paper at the beginning of class on the due date. Refer to the articles (the original two, as well as at least four others) within the abstract and clip all of the articles to the back. The presentation is your verbal capsule thereof, where you will describe your articles in a short speech.

The abstracts will be evaluated on their clarity, organization, and interest, as well as their spelling, grammar, referencing, and formatting. Just as in the abstracts for your lab reports, include content, motivation, methodology, important results, and implications of those results. The presentations (both for projects and literature reviews) will be evaluated on their timeliness, quality of the visuals, quality of the delivery, clarity, organization, interest, and responses to questions.

Writing Center

Located on the first floor of Daniels Hall (room 116), the Writing Center is a valuable resource for helping you improve as a writer. Writing Center tutors are your peers (other undergraduate and graduate students at WPI) who are experienced writers themselves and who enjoy helping others tackle thinking/writing challenges. Although a single tutoring session should never be seen as a quick fix for any writing difficulty, these sessions can help you identify your strengths and weaknesses, and teach you strategies for organizing, revising, and editing your course papers, projects, and presentations. Writing Center services are free and open to all WPI students in all classes, and tutors will happily work with you at any stage of the writing process (early brainstorming, revising a rough draft, polishing sentences in a final draft). Visit the Writing Center website <wpi.edu/+writing> to make an appointment.

Communication, etc.

I assume that you read your email at least once each business day. You may assume the same for me. If you have computer or network problems, it is still your responsibility to keep up with course announcements. I also assume that you have read and understood everything in this document. If you need to talk to me, the best time is right after class. My email address is nab@wpi.edu , telephone 508-831-5365, fax 508-831-5886, office Olin Hall 219, mailbox near the Physics Department office, web address for this page www.wpi.edu/~nab/PH561.html.

If you need course adaptations or accommodations because of a disability or if you have medical information to share with me, please see me. Students with disabilities are encouraged to contact the Disability Services Office (DSO) as soon as possible to ensure that such accommodations are implemented in a timely fashion. The DSO is located in Daniels Hall, (508) 831-5235.

Individual integrity is vital to the academic environment because education involves the search for and acquisition of knowledge and understanding, which are, in themselves, intangible. Evaluation of each student’s level of knowledge and understanding is a vital part of the teaching process, and requires tangible measures such as reports, examinations, and homework. Any act that interferes with the process of evaluation by misrepresentation of the relation between the work being evaluated (or the resulting evaluation) and the student’s actual state of knowledge is an act of academic dishonesty. The moral equivalent of academic dishonesty in larger society is treason.

Important times, places, and dates

Return to:

AFM | Grading | Calendar | Prelabs and labs | Other work | Writing Center | Communication and dates

  January 2018