Atomic Force Microscopy

PH 597A, Atomic Force Microscopy

Spring 2008
Prof NA Burnham, Physics Department
nab@wpi.edu , X-5365, OH 219
www.wpi.edu\~nab\PH597A.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 semester emphasizes instrumentation, the second half interpretation. A bachelor's degree in science or engineering is sufficient background. Previous students have indicated that the course was not only helpful to their research, but also in finding employment. 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 gain an understanding and appreciation of scientific research
To develop the ability to write a good lab report

Grading

Here is the grading scheme:

Type of Assignment	# x % (Min.Words)
The six instrument lab reports	3 x 4 % (400) 2 x 8 % (800) 1 x 12 % (1200)
The two exams	2 x 10 %
The six computer lab reports	10 % (200)
Your lecture	10 %
Abstract and presentation	10 %
Responsibility, timeliness, cooperation	10 %

Syllabus

IL = Instrument Lab, CL = Computer Lab. This is the syllabus for the undergraduate course, which has 21 class meetings, 7 computer labs, and 6 instrument labs.

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

Calendar

Here is the graduate calendar. We will cover the same material as the undergraduates in 14 classes, 6 computer labs, and 6 instrument labs. The shaded topics are those of the second exam.

Week	Date	Topic	Lecturer 9-10:00	Grp1, 10-12:00	Grp2, 10-12:00	OffHr 11-12:00	Due
				(Students 1,3,5)	(Students 2,4,6)
1	14-Jan	Introduction	NAB	IL1	CL1	Open	–
2	21-Jan	Feedback and artifacts	NAB	CL1	IL1	1. Saonti Charkraborty	–
3	28-Jan	Noise and FFTs	1. Saonti Charkraborty	IL2	CL2	2. Lisa Lee	CL1, IL1
4	4-Feb	Calibration	2. Lisa Lee	CL2	IL2	3. Nihar Pradhan	–
5	11-Feb	STM, LFM	3. Nihar Pradhan	IL3	CL3	4. Paola Pinzon-Arango	CL2, IL2
6	18-Feb	Other SPMs and modes	4. Paola Pinzon-Arango	CL3	IL3	5. Anusha Pokhriyal	–
7	25-Feb	UFk, force curves	5. Anusha Pokhriyal	IL4	CL4	6. Jason Cox	CL3, IL3
–	3-Mar	–	–	–		–	–
8	10-Mar	Surface forces	6. Jason Cox	CL4	IL4	Open	Topic
9	17-Mar	Exam 1	–	IL5	CL5	Open	CL4, IL4
10	24-Mar	Mechanical properties	NAB	CL5	IL5	Open	3 Papers
11	31-Mar	Contact mechanics	NAB	IL6	CL6	Open	CL5, IL5
12	7-Apr	Molecular dynamics	NAB	CL6	IL6	Open	Abstract
13	14-Apr	Exam 2	–	If unavoidable, make-ups		Open	CL6, IL6
14	21-Apr	20-min. presentations by all students, 9:00-12:00					Presentation

Learning objectives

What follows are the objectives for the seven units of the course (undergraduate version). The first graduate exam covers Units 1-4, the second Units 5-6. 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. 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
PH2510, Atomic Force 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 .

Reading, lecture, abstract, and presentation

I would like you each to take one lecture. See me the week before your scheduled time to review the material.

The presentation is a means for you to explore a subject that interests you. You will synthesize at least six related articles in cogent fashion for me and the rest of the class. The one-page abstract will reflect your understanding of the articles. It should be at least 250 and fewer than 500 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. Computer projection will be available, although it might not be tied into the network

I will post your weekly reading here:

Date	Reading	Objectives
For 21 Jan:	Syllabus; PG Intro; PG Sections 1.0, 1.1, 1.7; PG Chapter 5, IntroAFM, IntroNST, PH2510, LP, EXP	1a-e
For 28 Jan:	PG Chapter 4, UGI Chapter 4, FB	1f-2d
For 4 Feb:	DraftSect2.2	2e-2g
For 11 Feb:	PG Chaps 2 and 3, StiffCal	4a-4e
For 18 Feb:	HLI, HLII, STM, FFM	3a-3c
For 25 Feb:	PG Sects. 1.2-1.6	2h, 3d, 3e
For 10 Mar:	Draft Sect. 4.1	5a-5d
For 17 Mar:	SFA Sects. 1-3 EXAM 1	6a-6c
For 24 Mar:	--	--
For 31 Mar:	MPM	6e
For 7 Apr:	SFA Sects. 4.0-4.2	6d, 6f, 6g
For 14 Apr:	SFA Sects. 4.3-5.2 EXAM 2	6g, 6h
For 21 Apr:	-- PRESENTATIONS	--

Laboratories

Labs are worth 50 % 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.

I will answer questions concerning the self-paced computer labs during our regularly scheduled sessions. 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 Dr Deli Liu, deli@wpi.edu, OH 220, X-5391, who is my postdoc.

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. If you fail to comply with the laboratory procedures, you will not be permitted to use the lab; you will not pass the course.

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 the computer labs, 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\PH597A.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

The course is held Mondays 9-12:00 in Olin Hall. We start with an hour lecture in OH214, then split into two groups. One group does a computer lab in OH208, the other an instrument lab in OH009. We meet every Monday from January 14 to April 21, with the exception of March 3.

January 2008