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PH 2510, Atomic Force Microscopy

C Term 2022
Prof NA Burnham, Physics Department
nab@wpi.edu , X5365, 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:

The overall goal of the course is not only to provide you with a valuable skill (AFM), but to help you develop your critical thinking and scientific communication skills such that you will be well prepared for an MQP and your career--no matter your major, no matter if you use AFM in your MQP or not.

AFM | Grading | 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 %

IL, instrument lab reports
3 x 4 % (400)
2 x 8 % (800)
1 x 12 % (1200)

EX, exams 2 x 10 % 50
PP/PA/PR, project proposal, abstract, presentation 1 %, 3 % (300), 4% 5
CL, computer lab reports 7 x 2 % (200) 5
ML, "macro"-lab reports
6 x 1 % (100) 5
Q, quiz questions
16 x 6/16 %

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. The twenty-point scale is enumerated in the rubric available in the Instrument Lab Materials folder in the Files section at our Canvas site. If your final letter 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 Peer Learning Assistants grade most of your submissions. I grade your exams and presentation-related work.  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 us as having high expectations for you.  After the first exam, I will give you an indication of how well you are doing.

In C22, we have the collective challenge of the easily transmissible Omicron variant of Covid.  If one of us tests positive, we have to isolate for five--or maybe even ten--days.  That's a lot out of a seven-week course!  So if we stay in touch with each other about our respective situations, we will try to find ways to work with the tight schedule.  I would like each of you to learn a lot and be successful.

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. Italics show the six instrument labs and seven computer labs.  Bold indicates an assignment that is due.  Remember that Pre-Labs are to be printed on paper and brought to the beginning of your lab session so that you'll be allowed to perform the lab.  Quizzes and presentations (PR) are due at 11:30 AM on the respective days.  Other submissions are due before midnight on the indicated day.
Week of Monday
IS 105 (mostly)
IS 105 (mostly)
Instrument Lab
OH 009, Tues or Weds
IS 105
Computer Lab (mostly)
GH 012  Fridays (mostly)
9 January 2022

Introduction on "Monday"
Feedback and artifacts
16 January

CL1. Image processing
Meet in OH 114
IL1. Laboratory procedures
Perturbations and noise
Q4, CL1
CL2. Feedback and noise
23 January
Q6, IL1
IL2. Acquiring
Q7, CL2
30 January
Other modes
Probe calibration
Q9, IL2
IL3. Optimizing
Scanner calibration
Q10, CL3
UFk Meet in IS 105
Q11, ML3
6 February
CL4. UFk
Meet in OH 114
Force curves
Q12, IL3
IL4. Calibration
CL5. Stiffness
13 February
Mechanical properties
Surface forces
Q14, IL4
IL5. Force curves
Contact mechanics
Q15, CL5
CL6. Contact mechanics
20 February
Molecular dynamics
IL6. Contact mechanics
Advising Day, Make-up labs? 

Reading Day, Make-up labs?  ML6, PA
27 February
Student talks
Student talks
Make-up labs?
Visit other AFMs on campus
CL7. Molecular dynamics


Described here are the prelabs and the three different types of labs.  The purpose of prelabs is to prepare you for the instrument labs, the heart of the course that will allow you to state that you know how to operate an AFM.  However, they are "expensive," in the sense that one PLA is assigned for just one small team of students.  Therefore, the time available for instrument labs is restricted, and other means to help you learn the course material are necessary.  This is the role of the computer and macro-labs, which provide different approaches to the topics.

Each prelab is worth 1 % of your final grade.  They are based on your understanding of the video tutorials and the instructions.  Find what you have to do in the instrument lab instructions at our Canvas site. 

Between lab reports and prelabs, 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 lab reports.  You will work individually on the computer and submit individual computer lab reports.  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 GH 012 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.  Any of the almost four-hundred public computers on campus offer 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 purpose of the macro-labs is to demonstrate important course concepts in a hands-on, visual way.

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.  And now that you have practiced the skill and art of report writing in the first part of the term, this last lab report is worth 12 % of your final grade.  The grading rubric will be posted at Canvas.  If you have a question about the labs as you write your reports, see me, or talk to one of the PLAs.  They are:  Brigitte N Lefebvre, bnlefebvre@wpi.edu and Samuel P Skinner, spskinner@wpi.edu.

You must attend 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 over the Advising/Reading Day weekend and the last full week of the term.  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.  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, submit two related publications that interest you about modern materials, biophysics, or nanotechnology.  At least one article must be from a 2017 or later peer-reviewed journal.  (No web sites unless they are web versions of peer-reviewed 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.  Refer to the articles within the abstract.  The presentation is your verbal capsule thereof, where you will describe your articles in a short speech; this is uploaded to Canvas prior to the start of class.  Participation in the presentations is contingent upon timely submissions of a presentation proposal and an abstract (just as for a real, professional conference). The grading rubrics for the abstracts and presentations will be posted at Canvas.

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 in the hallway between OH 118 and 119, web address for this page www.wpi.edu/~nab/PH2510.html, and my Outlook calendar is usually up to date for about a week ahead.  If you would like an appointment, please send me an Outlook invitation for a time of mutual availability, instead of initiating an endless email thread.

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 studentís 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 studentís actual state of knowledge is an act of academic dishonesty. Academic dishonestry includes both intended and unintended plagiarism.

Important times, places, and dates

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

January 2022