Atomic Force Microscopy

PH 2510, Atomic Force Microscopy

D Term 2010
Prof NA Burnham, Physics Department
nab@wpi.edu , X-5365, OH 219
www.wpi.edu\~nab\PH2510.html

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. You must pass the course in order to use the AFM 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.

Course objectives

To become competent in the use of AFMs and in the interpretation of AFM data, skills that you might one day use as a professional
To learn how physics applies to AFMs
To develop the ability to write a good lab report
To gain an understanding and appreciation of scientific research

Grading

Here is the grading scheme:

Type of Assignment	# x % (Min.Words)	Comments	Pts.
PL, prelabs	6 x 1 % (100)	REQUIRED, no lab time until PL done to acceptable level	5
IL, instrument lab reports	3 x 4 % (400) 2 x 8 % (800) 1 x 12 % (1200)	REQUIRED, missed lab = -3.0 % of final grade, late reports -1 pt/day (before 16:00), each lab report must be done to an acceptable level	20
EX, exams	2 x 10 %	REQUIRED, missed exam = -1.5 % of final grade	50
PP/PA/PR, project proposal, abstract, presentation	1 %, 3 % (250), 6%	late work not accepted	5
HW, homework	4 x 2.00 %	late work not accepted	5/prob
CL, computer lab reports	7 x 1.43 % (200)	late work not accepted	5
RS, reading summaries	6 x 1.00 % (300)	late work not accepted	10

Here is how to interpret the grading scales:


Rating	5-pt scale	20-pt scale
acceptable	3	11, 12
good	4	13, 14
very good	5	15, 16
excellent	-	17, 18
masterful	-	19, 20
Approach:	global	itemized

The two-point and five-point scales are done globally, meaning that your grade depends on the overall quality of your work. The twenty-point scale is itemized, meaning that points will be taken off according to specific things that are wrong. Assignments shorter than the minimum word count will be returned ungraded. Electronic submissions of anything except homework will suffer a 20 % grade penalty.

Of the thirty-four times that we will meet, only eight times is your attendance essential – the six instrument labs and the two exams. For each of the six required lab sessions that you miss, a three percent penalty on your final grade will be assessed. Missing an exam costs you 1.5 % of your final grade. 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 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 labs, presentation, and homework. 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 prelabs and computer lab reports on five-point scales. They also grade the instrument lab reports, which are then checked by me. I grade your homework, presentation abstracts, presentations, and exams. 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, 85 or above is an A, 70 or above B, and 55 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. During the fifth week of the course, I will give you an indication of how well you are doing.

Syllabus

IL = Instrument Lab, CL = Computer Lab.

PART I – INSTRUMENTATION

Unit 1, Fundamentals of imaging

Class 1: Introduction
Class 2: SPM and AFM instrumentation
IL1: Laboratory procedures
CL1: Image processing
IL2: Acquiring an image

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

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

Class 13: Exam 1 on instrumentation

PART II – INTERPRETATION

Unit 5, Force-curve mechanics

Class 11: Potentials, forces, and stiffnesses
Class 12: Force curves
IL5: Acquiring and processing force curves
CL4: Potentials, forces, and stiffnesses
CL5: Compliance

Unit 6, Tip-sample interactions

Class 14: Surface forces
Class 15: Basic mechanical properties
Class 16: Contact mechanics
Class 19: Energy dissipation and molecular dynamics
IL6: Contact mechanics
CL6: Contact mechanics
CL7: Molecular dynamics

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, HW = Homework, IL = Instrument Lab, CL = Computer Lab, EX = Exam, PP = Presentation Proposal, PA = Presentation Abstract, PR = Presentation, DDD = Drop-Dead Day. 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 six units referred to above.

Week of	Monday	Tuesday	*Instrument Lab* Tues or Weds in OH 009	Thursday	Computer Lab Fridays in HL230	% this Week
14 March 2010	Introduction --	Instrumentation --	IL1. Laboratory procedures PL1	Feedback and artifacts RS1	CL1. Image processing --	1.6 %
21 March	Perturbations and noise RS2	FFTs IL1	IL2. Acquiring PL2	STM HW1	CL2. Feedback and noise CL1	8.0 %
28 March	LFM RS3	Other modes IL2	IL3. Optimizing, LFM PL3	Probe calibration PP	CL3. FFTs CL2	8.0 %
4 April	Scanner calibration RS4	UFk IL3	IL4. Calibration PL4	Force curves HW2	CL4. UFk CL3	8.0 %
11 April	Surface forces RS5	EX1, IL4	IL5. Force curves PL5	Mechanical properties PA	CL5. Stiffness CL4	26.7 %
18 April	Patriot's Day, no class --	Contact mechanics IL5	IL6. Contact mechanics PL6	Project presentation day, no class, HW3	CL6. Contact mechanics CL5	13.7 %
25 April	Student talks PR	Student talks PR	If unavoidable, make-up labs, due on Tuesday. RS6	Molecular dynamics IL6	CL7. Molecular dynamics CL6	17.3 %
2 Mayl	Review HW4	EX2 CL7	DDD			17.3 %

Learning objectives

What follows are the objectives for the seven units of the course. The first exam covers Units 1-4, the second Units 5-7. The keywords used below are defined in the next section.

Unit 1, Fundamentals of imaging

1a. Describe the differences among SPM, SXM, STM, AFM, SFM, LFM, and FFM. (PG Sects.1.0, 1.1)
1b. Know in which environments an SPM can operate. (PG Sect.1.7)
1c. Sketch diagrams showing the difference between constant-height and constant-strength modes. (PG Sects.1.0, 1.1)
1d. State the advantages and disadvantages of AFM and the ways in which AFM can be used. (IntroAFM)
1e. Distinguish between the "top-down" and "bottom-up" approaches to nanotechnology. (IntroNST)
1f. Know the effects of the basic image-processing options. (SPMLab, CL1)
1g. Describe how to acquire and process a contact-mode constant-normal-force AFM image. (PG Chap.5, UGI Chaps. 1-3, IL1, IL2)

Unit 2, Difficulties of imaging

2a. Describe how a feedback circuit works and how you can control it. (UGI Chap.4, FB, CL2)
2b. Know how to optimize an image. (UGI Chap.4, IL3)
2c. Know how to test for artifacts. (PG Chap.4, UGI Chap.4)
2d. Identify common artifacts and be able to rectify them. (PG Chap.4, UGI Chap.4)
2e. Identify the four most important types of noise and specify their characteristics. (DraftSect2.2, CL2 )
2f. Know how SPMs are built, situated, and protected so as to limit perturbations. (DraftSect.2.2)
2g. Explain the principles of fourier theory and fourier threshold filtering. (DraftSect2.2, CL3)
2h. Be able to improve SPM images using fourier threshold filtering. (CL3)

Unit 3, Other SPMs and operational modes

3a. Know the basic physical principles behind STM. (HLI, STM)
3b. Know how static and sliding friction are determined from a friction loop and what influences them. (PG Sects.1.2-1.6, HLII, FFM, IL3)
3c. Given the topography and friction coefficients of a hypothetical surface, sketch the expected friction loop. (PG Sects.1.2-1.6, HLII, FFM, IL3)
3d. Describe the contact, noncontact, and intermittent-contact modes and know why they are used. (PG Sects.1.2-1.6)
3e. List the advantages and disadvantges of the contact, noncontact, and intermittent-contact modes. (PG Sects.1.2-1.6)

Unit 4, Calibration

4a. Discuss why probes are the size and shape that they are, and why they are primarily made from silicon and silicon nitride. (PG Chap.3)
4b. Describe to calibrate the spring constant of a cantilever. (PG Chap.3, StiffCal, IL4)
4c. Describe how to calibrate tip size and shape. (PG Chap.3, IL4)
4d. Describe the problems of piezoelectric scanners and how to correct for them. (PG Chap.2, IL4)
4e. Describe how to calibrate a scanner. (PG Chap.2, IL4)

Unit 5, Force-curve mechanics

5a. Calculate all the relationships among potentials, forces, and concavity. (DraftSect4.1, CL4)
5b. Understand the origins of cantilever instabilities. (DraftSect4.1, CL5)
5c. Understand why and how raw force-curve data is converted into processed data. (DraftSect4.1)
5d. List the advantages and disadvantages of weak and stiff cantilevers. (DraftSect4.1)

Unit 6, Tip-sample interactions

6a. Distinguish between surface forces and adhesion. (SFA)
6b. Memorize the equation for the van der Waals force between a sphere and a flat. (SFA)
6c. Understand the features of a force curve due to meniscus and capillary formation. (SFA)
6d. Identify the principal features of a force vs depth curve. (SFA, CL6, IL5, IL6)
6e. Know what v, E, and stress-strain curves are and how they are measured. (MPM)
6f. Memorize and be able to manipulate and use the Hertz equations for K, P, a, and delta. (SFA, CL6)
6g. Distinguish among elasticity, anelasticity, adhesion hysteresis, and plasticity. (SFA)
6h. Know the advantages and disadvantages of the continuum versus molecular dynamics approaches. (SFA, CL7)

Unit 7, A glimpse at current research

7a. Give some examples of current research topics. (student presentations)
7b. Know how SPMs have contributed to this research. (student presentations)

Study materials

Some of the study materials are protected; you must be on campus or connected via the Virtual Private Network in order to download them. You may borrow a notebook of the printed material from the Physics Department Office, for your reading in the Physics Library, OH 118. The keywords for the materials are:

Reading materials

Lab materials

DraftSect2.2, Combating Unwanted Perturbations
DraftSect4.1, Force Curves
FB, Feedback System Response in a Scanning Tunneling Microscope
FFM, Friction Force Microscopy
HLI, Looking at Atoms
HLII, Stroking Molecules
IntroAFM, Poster introducing AFM
IntroNST, Poster introducing nanoscience and technology
MPM, Mechanical Properties of Metals
PG, A Practical Guide to Scanning Probe Microscopy
SFA, Surface Forces and Adhesion
StiffCal, Stiffness calibration paper
STM, Scanning Tunneling Microscopy

CLI, Computer Lab Instructions
Data Dlevers.pdf, Data sheet for stiff cantilevers
Data gratings, Data sheet for calibration gratings
Data Ultralevers.pdf, Data sheet for compliant cantilevers
EXP, Expectations of AFM Users
ICA, I.C.Adams manual *
ILI, Instrument Lab Instructions
ILR, Template for Instrument Lab Reports
Lab5, Excel file for Lab 5 report
Lab6, Excel file for Lab 6 report
LP, Laboratory Procedures
SPMLab, Image Analysis Menu Items (Chaps 4-6) *
UGI, User's Guide for the M5 Instrument, Part I (Chaps 1-4) *
UGII, User's Guide for the M5 Instrument, Part II (Chapter 4) *

* The asterix indicates that the document is long and might not be worth printing.

Should you need the complete references for these articles, please find them here .

Prelab assignments and labs

The six prelabs 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 (>= 3 out of 5 pts). Please give your prelab to the TA at the beginning of your instrument lab. Each prelab, 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 60 % of your final grade. You will work in teams of two 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. 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 in the Study Materials section, and figures should be on separate sheets of paper, stapled to the back of the reports. Find out what to do in the Computer Lab Instructions and Instrument Lab Instructions respectively. Click here for the Instrument Lab Schedule .

I will answer questions concerning the self-paced computer labs during our regularly scheduled sessions in HL 230 on Fridays at 12:00. If you miss a session, no help will be given to you and 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.

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 TAs. They are Ms Saonti Chakraborty, saonti@wpi.edu, OH 114, X-5758, and Mr Nihar Pradhan, nihar@wpi.edu, OH 004, X-5282. Ms Deli Liu, deli@wpi.edu, OH 220, X-5391, is my postdoc and can help you if you cannot find the regular TAs or me.

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 3 % of your final grade. 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.

Homework, presentation proposal, presentation, and presentation abstract

No late homework will be accepted, independent of the reason. The homeworks are reading assignments, about which you are to write a summary paragraph(s), adding a question or comment about the material or a request for me to explain something in class. Please put your questions, comments, and requests at the end of your text. This is due to me by email, in plain, unformatted text (no attachments), at least two hours before class. Please begin your emails with an appropriate subject line, e.g., PH2510 HW1. If the network is down, please bring your homework to class on paper. I will use your questions and comments as feedback. The summary, although you submit it to me, should be written for your own benefit, so that you can use it as a study aid while preparing for the exams. (A set of notes is fine.) Use the learning objectives above to help you pick out the important points. Each homework, graded out of two points, is worth 0.33 % of your final grade. You will receive full credit for 15 out of the 17 assignments; i.e. you may skip two assignments without affecting your grade.

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 2000 or later peer-reviewed journal. (No web sites unless they are web versions of hard-copy journals. A good place to start is www.vjnano.org. 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 you to 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 at least 250 and fewer than 500 words in length, using the same formatting as the abstract in the template for the instrument lab reports, and submitted on paper at the beginning of class on the due date. Refer to the articles within the abstract and staple the articles to the back. The presentation is your verbal capsule thereof, where you will describe your articles in a short speech. You may also come to the blackboard or use the overhead projector.

Homework	Assignment
HW1, Basic instrumentation	Syllabus; PG Intro; PG Sections 1.0, 1.1, 1.7; PG Chapter 5
HW2, Nanoscience	IntroAFM; IntroNST
HW3, Feedback and artifacts	PG Chapter 4; UGI pp 4-11 to 4-15; FB
HW4, Perturbations and noise	DraftSect2.2, Sections 2.2.1-2.2.2
HW5, FFTs	DraftSect2.2, Section 2.2.3
HW6, STM	HLI; STM
HW7, LFM	HLII; FFM
HW8, Other modes	PG Sections 1.2-1.6
HW9, Probe calibration	PG Chapter 3; StiffCal
HW10, Scanner calibration	PG Chapter 2
HW11, UFk	DraftSect4.1, Sections 4.1.1-4.1.2
HW12, Force curves	DraftSect4.1, Sections 4.1.3-4.1.4
HW13, Surface forces	SFA Sections 3.0-3.6
HW14, Mechanical properties	MPM
HW15, Contact mechanics	SFA Sections 4.0-4.2
HW16, Molecular dynamics	SFA Sections 4.3-5.2
HW17, Review	Send me two review questions about the second half of the course.
PP, Presentation Proposal	Bring me hard copies of at least two related current (2000+) publications that interest you about modern materials, biophysics, or nanotechnology. At least one article must be from a peer-reviewed journal. The other may be from a popular science source, such as the New York Times or Discovery Magazine. If one article refers to the other, the two articles likely concern the same topic. For peer-reviewed journals, a good place to start is www.vjnano.org . 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.
PA, Presentation Abstract	The presentation abstract will reflect your understanding of the articles. It should be at least 250 and fewer than 500 words in length, using the same formatting as the abstract in the template for the instrument lab reports, and submitted on paper at the beginning of class on the due date. Refer to the articles within the abstract and staple the articles to the back.
PR, Presentation	Be ready to describe your articles in a short verbal presentation. You may come to the blackboard or use the overhead projector.
DDD, Drop-Dead Day	All IL and EX work must be submitted before noon on 1 May 2008 in order to be included in your D-term grade.

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. The moral equivalent of academic dishonesty in larger society is treason.

Important times, places, and dates

Classes are held MTThF at 12:00.
Prelab assignments are due at the beginning of your instrument lab sessions. Lab reports must be submitted at the beginning of class or placed in my mailbox by 11:50. Homework is due to me at least two hours before class by email, or on paper in class if you have network problems.
Monday, Tuesday, and Thursday classes are in Olin Hall 223.
The fifty-minute computer labs are in Higgins Lab 230 on Fridays.
The two-hour instrument labs are held in Olin Hall 009 Tuesday afternoons and Wednesdays.

January 2008