[WPI banner]

PH 2510, Atomic Force Microscopy

D Term 2017
Prof NA Burnham, Physics Department
nab@wpi.edu , X-5365, 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:



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


Grading

Here is the grading scheme:
 

Type of Assignment
# x % (Min.Words)
Comments
Pts.
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

20
EX, exams 2 x 10 % REQUIRED, missed exam = -1n % of final grade, where n is the number of missed exams
50
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.
5
CL, computer lab reports 7 x 2 % (200) late work not accepted
5
ML, "macro"-lab reports
6 x 1 % (100) late work not accepted 5
D, discussion and quiz questions
16 x 6/16 %
late work not accepted



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.  A two-point scale is used for your contributions to the discussion questions:  one point means that I think your contribution is not thoughtful, two points means that it is.  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, 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 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.

Syllabus

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

PART I – INSTRUMENTATION

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
Unit 4, Calibration
Class 9:  Probe calibration
Class 10:  Scanner calibration
IL4:  Probe and scanner calibration
ML3:  Dynamic spring constant
Class 15:  Exam 1 on instrumentation


PART II – INTERPRETATION
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 research
Class 17:  Student presentations on current research
Class 18:  Student presentations on current research
Class 20:  Review
Class 21:  Exam 2 on interpretation

The above is summarized by this calendar.

PL = Prelab Quiz, IL = Instrument Lab, CL = Computer Lab, ML = Macro Lab, D = Discussion, 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
T or W in OH 114
Thursday Computer Lab
SL 123
% This Week
12 March 2017 Introduction
D1
Instrumentation
D2
IL1. Laboratory procedures
PL1
Feedback and artifacts
D3
CL1. Image processing
ML1
3.13 %
19 March
Perturbations and noise
CL1, D4
FFTs
IL1, D5
IL2. Acquiring
PL2
STM
D6
CL2. Feedback and noise
ML2

9.13 %
26 March LFM
CL2, D7
Other modes
IL2, D8
IL3. Optimizing, LFM
PL3
Probe calibration
D9
CL3. FFTs
ML3
9.13 %
2 April
Scanner calibration
CL3, D10
UFk 
IL3, D11
IL4. Calibration
PL4
Force curves
D12
CL4. UFk
ML4
9.13 %
9 April Mechanical properties
CL4, D13
Surface forces
IL4, D14
IL5. Force curves
PL5
EX1
--
CL5. Stiffness
ML5, PP, CL5*
25.75 %
16 April Patriot's Day, no class
Contact mechanics
IL5
, D15
IL6. Contact mechanics
PL6
Project presentation day, no class
CL6. Contact mechanics
ML6, PA
13.38 %
23 April Student talks
CL6, PR

Student talks 
PR
If unavoidable, make-up labs
--
Molecular dynamics
D16
CL7. Molecular dynamics
IL6
18.38 %
30 May
Review
CL7
EX2
--

 
 
12.00 %
* CL5 would ordinarily be due on Monday, but Olin Hall might be closed that day because of the Patriot's Day holiday. Whereas all other CLs are due by noon, CL5 is due at 8 pm on Friday in my mailbox, between OH 118 and 119.

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 myWPI 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, but you will submit individual instrument lab reports.  You will work individually on the computer and macro-labs and submit individual 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 template provided at myWPI.  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 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 equipment for the macro-labs is in OH 114, the same room as our lab room.  You have access to it during the PH 2510 lab hours, Tuesdays 1-5:00 and Wednesdays 9-5:00.  The macro-lab reports are due on Fridays at the beginning of our computer lab sessions in SL 123. 

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 TA.  He is Peter Melander, pdmelander@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 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.  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


March 2017