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PH 2510, Atomic Force Microscopy

C Term 2024
Prof NA Burnham, Physics Department
nab@wpi.edu , X5365, OH 219
www.wpi.edu\~nab\PH2510.html

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.

Grading

 

Type of Assignment

# x % (Min.Words)

Pts.

PL, prelab quizzes

6 x 1 %

5 

IL, instrument lab reports

3 x 4 % (400)
2 x 8 % (800)
1 x 12 % (1200)


20

EX, exams

2 x 10 %

50

PP/PA/PR, project proposal, abstract, presentation

1 %, 3 % (300), 4%

5

CL, computer lab reports

6 x 2 % (200)

5

ML, "macro"-lab reports

6 x 1 % (100)

5

Q, quiz questions

16 x 8/16 %

5 

 

Here is how to interpret the grading scale:

Rating

5-pt scale

Suggests competence

2

Demonstrates competence

3

Suggests mastery

4

Demonstrates mastery

5


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 Lab Materials module 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 PLAs/Tas 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.

 

 

 


Here is the schedule.

PL = Prelab Quiz, IL = Instrument Lab, CL = Computer Lab, ML = Macro Lab, Q = Quiz on Canvas, PP = Presentation Proposal, PA = Presentation Abstract, PR = Presentation. Italics show the six instrument labs and six computer labs.  Bold indicates an assignment that is due.  Pre-class quizzes (Q) and presentations (PR) are due at 11:30 AM on the respective days; Pre-lab quizzes (PL) before you begin your Instrument Labs.  Other submissions are due before midnight on the indicated day.

 


 

Week of

Monday
HL 202 (mostly)

Tuesday
HL 202

Instrument Lab
OH 009, Tues or Weds

Thursday
HL 202

Computer Lab (mostly)
Fridays AK 013 (mostly)

7 January 2024

Introduction on "Monday"
Q1 

Instrumentation
Q2 

CL1. Image processing

14 January

Feedback and artifacts

Q3

IL1. Laboratory procedures
PL1

Perturbations and noise
Q4, CL1

CL2. Feedback and noise
ML1

21 January

FFTs
Q5

STM
Q6, IL1

IL2. Acquiring
PL2

LFM
Q7, CL2

CL3. FFTs
ML2

28 January

Other modes
Q8

Probe calibration
Q9, IL2

IL3. Optimizing
PL3

Scanner calibration
Q10, CL3

UFk Meet in OH 109
Q11, ML3

4 February

CL4. UFk
Meet in SL 123

Force curves
Q12, IL3

IL4. Calibration
PL4

EXAM 1
ML4

Wellness Day Make-up labs?

11 February

Mechanical properties
Q13

Surface forces
Q14, IL4

IL5. Force curves
PL5

Contact mechanics
Q15, CL4

CL5. Stiffness

ML5

18 February

Molecular dynamics
Q16

EXAM 2

IL6. Contact mechanics
PL6

Advising Day, Make-up labs?  CL5, PP

CL6. Contact mechanics 

ML6, IL5

25 February

Visit other AFMs

Visit other AFMs, PA

Make-up labs? Bring your own sample? PR

Student talks
PR, CL6

Student talks
IL6

 

Labs

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 or TA is assigned for just one small team of students.  Therefore, the time available for instrument labs is restricted, and other means have been created to help you learn the course material.  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 Lab Materials module 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 labs and submit individual computer lab reports.  Instrument lab reports should use the provided template.  Instructions and the template reside in the Lab Materials module at our Canvas site.

I will answer questions concerning the self-paced computer labs during our regularly scheduled sessions in AK 013 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 on Canvas in the Lab Materials module.  If you have a question about the labs as you write your reports, see me, or talk to one of the PLAs/TAs.  They are:  Michelle C Sangillo, mcsangillo@wpi.edu and Justin Y Burton, jyburton@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 Days 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 2019 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 in the Class Materials module 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 any time. 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, 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. I’m also trying Calendry for the first time, https://calendly.com/nab-wpi/30min.

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 Accessibility Services Office as soon as possible to ensure that such accommodation is provided in a timely fashion. It is 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 dishonesty includes both intended and unintended plagiarism.

Important times, places, and dates