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PH 2510, Atomic Force Microscopy

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

Link to YouTube lessons

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.  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 | Syllabus | Calendar | Objectives | Materials | Prelabs and labs | HW and presentation | Communication and dates


Here is the grading scheme:

Type of Assignment
# x % (Min.Words)
PL, prelab quizzes
6 x 1 %
REQUIRED, if you fail a quiz, you must pass a second, harder quiz before your next lab period.  If you fail the second quiz, you fail the course.

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 level

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
ML, "macro"-lab reports
6 x 1 % (100) late work not accepted 5
Q, quiz questions
16 x 6/16 %
late work not accepted

Here is how to interpret the grading scale:

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

The five-point scale 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.  If your final grade is near the border between two grades, e.g. between A and B, then your participation and enthusiasm will decide 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 and macro-labs, presentation, and discussions. But it is unlikely that you will do well on the exams if you ignore such a large fraction of the work.

The Teaching Assistants grade your prelab quizzes and computer and macro-lab reports.  They also grade the instrument lab reports, which are then checked by me.  I grade your other work.  I am repelled by point grubbing, but I certainly would like to see blatant errors on the part of the graders (myself included).  Nominally, 85 % or above is an A, 75 % or above B, and 65 % or above C.  These lower borderlines for grades might initially seem encouraging.  Yet I will be most pleased if you come to think of me as a demanding grader.  After the first exam, I will give you an indication of how well you are doing.

Of the thirty-four times that we will meet, only eight times 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.


IL = Instrument Lab, CL = Computer Lab, ML = Macro Lab.


Unit 1, Fundamentals of imaging
Class 1:  Introduction
Class 2:  SPM and AFM instrumentation
IL1:   Laboratory procedures
IL2:  Acquiring an image
CL1:  Image processing
ML1:  Static spring constant
Unit 2, Difficulties of imaging
Class 3:  Feedback and artifacts
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
Unit 3, Other SPMs and operational modes
Class 6:  Scanning tunneling microscopy
Class 7:  Lateral force microscopy
Class 8:  Operational modes
IL3:  Optimizing an image and lateral force microscopy
ML3: Frequency and amplitude shifts
Unit 4, Calibration
Class 9:  Probe calibration
Class 10:  Scanner calibration
IL4:  Probe and scanner calibration
ML4:  Dynamic spring constant
Class 15:  Exam 1 on instrumentation

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
ML5:  Cantilever instabilities

Unit 6, Tip-sample interactions

Class 14:  Surface forces
Class 16:  Contact mechanics
Class 18:  Molecular dynamics
IL6:  Contact mechanics
CL6:  Contact mechanics
CL7:  Molecular dynamics
ML6:  Force curve of an unknown sample

Unit 7,
A glimpse at current research
Class 17:  Student presentations on current research
Class 18:  Student presentations on current research
Class 19-21:  Exam 2 on interpretation (TBD)

The above is summarized by this calendar.

PL = Prelab Quiz, IL = Instrument Lab, CL = Computer Lab, ML = Macro Lab, Q = Quiz on Canvas, EX = Exam, PP = Presentation Proposal, PA = Presentation Abstract, PR = Presentation.   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 colors distinguish among the seven units referred to above.

Week of Monday  Tuesday Instrument Lab
OH 114
Computer Lab
OH 114
% This Week
11 March 2018 Introduction
IL1. Laboratory procedures
CL1. Image processing
Feedback and artifacts
3 %
18 March
Perturbations and noise
CL1, Q4
IL1, Q5
IL2. Acquiring
CL2. Feedback and noise
9 %
25 March LFM
CL2, Q7
Other modes
IL2, Q8
IL3. Optimizing

Probe calibration
9 %
1 April
Scanner calibration
CL3, Q10
IL3, Q11
IL4. Calibration
CL4. UFk
Force curves
9 %
8 April Mechanical properties
CL4, Q13
Surface forces
IL4, Q14
IL5. Force curves
CL5. Stiffness
25 %
15 April Patriots' Day (no class) CL5
Contact mechanics
, Q15
IL6. Contact mechanics
CL6. Contact mechanics
Project Presentation Day (no class)
15 %
22 April Student talks*
Molecular Dynamics
IL6, Q16
Bring-your-own sample day
CL7. Molecular dynamics
Self-study day
18 %
29 April
Exam 2
Visit GP AFM Lab

12 %
* Upload to Canvas

Prelab quizzes and labs

Each prelab quiz is worth 1 % of your final grade.  The quizzes are based on your understanding of the video tutorials and the instructions.  Find them at our Canvas site.  The TAs have the right to penalize your prelab grade if you are inattentive to laboratory procedures. 

Between lab reports and prelab quizzes, labs are worth 66 % of your final grade.  You will work in teams of two or three on the instrument and for macro-labs, but you will submit individual instrument lab reports.  You will work individually on the computer and submit individual computer lab reports.  All lab reports are to be printed on paper; electronic versions will be accepted with a 20 % penalty.  Instrument lab reports should use the provided template.  Instructions and the template reside at our Canvas site.

I will answer questions concerning the self-paced computer labs during our regularly scheduled sessions in OH 114 on Thursdays 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 equipment for the macro-labs is in OH 114, the same room as our lab room.  The macro-lab reports are due on Thursdays at the beginning of our computer lab sessions in OH 114. 

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 one of the TAs.  They are Zack Chester, zcchester@wpi.edu, and Thomas Marston, temarston@wpi.edu.

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.

Presentation proposal, presentation abstract, and presentation

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 2015 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.  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 your 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 one page, between 300 and 600 words in length, and submitted on paper at the beginning of class on the due date.  Refer to the articles within the abstract.  The presentation is your verbal capsule thereof, where you will describe your articles in a short speech.  Participation in the presentations is contingent upon timely submissions of a presentation proposal and an abstract.

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 will be evaluated on their timeliness, quality of the visuals, quality of the delivery, clarity, organization, interest, and responses to questions.

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, although you may try to find me at anytime. 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/PH2510.html, my schedule, including office hours, http://www.wpi.edu/~nab/Sched.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. Academic dishonestry includes intended and unintended plagiarism.

Important times, places, and dates

Return to:

AFM | Grading | Syllabus | Calendar | Objectives | Materials | Prelabs and labs | HW and presentation | Communication and dates

April 2018