Atomic Force Microscopy

PH 2510, Atomic Force Microscopy

D Term 2013
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. You must pass the course in order to use the AFMs 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.

The course objectives are:

To become competent in the use of AFMs and in the interpretation of AFM data,
To develop the ability to write a good lab report,
To gain an understanding and appreciation of scientific research, and
To learn how physics applies to AFMs.

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 = -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
HW, homework	6 x 2 % (200)	late work not accepted	20

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. 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 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. 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.

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, 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 seven units referred to above.

Week of	Monday	Tuesday	*Instrument Lab* T or W in OH 009	Thursday	Computer Lab SL 123	% This Week
10 March 2012	Introduction --	Instrumentation --	IL1. Laboratory procedures PL1	Feedback and artifacts --	CL1. Image processing HW1	3 %
17 March	Perturbations and noise CL1	FFTs IL1	IL2. Acquiring PL2	STM --	CL2. Feedback and noise HW2	9 %
24 March	LFM CL2	Other modes IL2	IL3. Optimizing, LFM PL3	Probe calibration --	CL3. FFTs HW3	9 %
31 March	Scanner calibration CL3	UFk IL3	IL4. Calibration PL4	Force curves --	CL4. UFk HW4	9 %
7 April	Mechanical properties CL4	Surface forces IL4	IL5. Force curves PL5	EX1 --	CL5. Stiffness PP, CL5*	24 %
14 April	Patriot's Day, no class	"Thursday" Contact mechanics IL5	IL6. Contact mechanics PL6	Project presentation day, no class, HW5	CL6. Contact mechanics PA	14 %
21 April	Student talks PR, CL6	Student talks PR	If unavoidable, make-up labs --	Molecular dynamics HW6	CL7. Molecular dynamics IL6	20 %
28 April	Review CL7	EX2 --	DDD			12 %

* 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.

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 (IWGN, IntroNST, IntroAFM, IL1, IL2, CL1, PG Chap.1&5; SPMLab, UGI Chap.1-3)

1a. Define the acronyms SPM, SXM, STM, AFM, SFM, LFM, and FFM.
1b. Know in which environments an SPM can operate.
1c. Sketch diagrams showing the difference between constant-height and constant-strength modes.
1d. State the advantages and disadvantages of AFM and the ways in which AFM can be used.
1e. Distinguish between the "top-down" and "bottom-up" approaches to nanotechnology.
1f. Know the effects of the basic image-processing options.
1g. Describe how to acquire and process a contact-mode constant-normal-force AFM image.

Unit 2, Difficulties of imaging (PG Chap. 4, DraftSects2.2-3, IL3, CL2, CL3; UGI Chap. 4, FB)

2a. Describe how a feedback circuit works and how you can control it.
2b. Know how to optimize an image.
2c. Know how to test for artifacts.
2d. Identify common artifacts and be able to rectify them.
2e. Differentiate between a magnitude spectrum and a power spectrum.
2f. Describe mean value, mean-square value, and root-mean-square value.
2g. Identify the four most important types of noise and specify their characteristics.
2h. Know how SPMs are built, situated, and protected so as to limit perturbations.
2i. Explain the principles of fourier theory.
2j. Distinguish between fourier threshold filtering and fourier frequency filtering.
2k. Be able to improve SPM images using fourier threshold filtering.

Unit 3, Other SPMs and operational modes (HLI, HLII, PG Ch.1, IL3, STM, FFM; UGII Chs.1&3, DraftChap7)

3a. Know the basic physical principles behind STM.
3b. Be able to explain why STM is so sensitive to distance and condition of the surface.
3c. Know how static and sliding friction are determined from a friction loop and the equations that define them.
3d. Given the topography and friction coefficients of a hypothetical surface, sketch the expected friction loop.
3e. Describe the contact, noncontact, and intermittent-contact modes and know why they are used.
3f. List the advantages and disadvantges of the contact, noncontact, and intermittent-contact modes.

Unit 4, Calibration (DraftSect4.1, PG Chap.2, IL4, kc_Exercise; StiffCal, UGII Chap. 6)

4a. Distinguish among the parts of a probe assembly.
4b. Understand why certain materials and geometries are used to construct probes.
4c. Discuss the phrases “range versus resolution” and “robustness versus resolution.”
4d. Describe the various ways in which tips and cantilevers are calibrated.
4e. Describe the problems of piezoelectric scanners and how to correct for them.
4f. Describe how to calibrate a scanner.

Unit 5, Force-curve mechanics (DraftChap5, IL5, CL4, CL5, FC_Exercise; MPM, UGII Chap. 4)

5a. Know the basic physical principles behind force curves — the relationships among potentials, forces, and concavity.

5b. Be able to determine if an equilibrium is stable, unstable, or neutral, both mathematically and by inspecting a potential diagram.
5c. Define monostability and bistability.
5d. Explain the origin of cantilever instabilities.
5e. Define a force curve.
5f. Understand how raw force-curve data is converted to processed data
5g. Discuss the limitations of weak cantilevers for force-curve aquisition.
5h. List and describe common problems with force curves.
5i. Compare and contrast elasticity, plasticity, and anelasticity.
5j. Sketch and discuss a stress-strain curve; define stress, strain, and elastic modulus.
5k. Define Poisson's ratio, reduced modulus, and indentation modulus.
5l. Define reduced radius, contact radius, and work of adhesion.

Unit 6, Tip-sample interactions (DraftSect6.1, SFA, IL5, IL6, CL6, CL7, ku_Exercise; StiffCalII, MDI, MDII)

6a. Distinguish between attraction and adhesion
6b. Describe the origin of van der Waals forces.
6c. Understand how the van der Waals potential takes different functional forms for different geometries.
6d. Be able to apply Eqs. 6.2 to specific substances.
6e. Interpret the features of a force curve due to meniscus and capillary formation.
6f. Calculate the work done in elongating a capillary, either with constant volume or with constant cross section.
6g. Sketch how the van der Waals and meniscus-capillary forces manifest themselves in force curves taken with weak and stiff cantilevers.
6h. Add to the van der Waals sketch for the previous objective the force values for unstable equilibria.
6i. State the functional dependence on delta of a flat, cone, and sphere indenting a smooth horizontal surface.
6j. Know and be able to manipulate the Hertz equations for K, P, a, ki, and delta.
6k. Describe how the Hertz equations change when surface forces are present.
6l. Sketch how force, contact radius, interaction stiffness, and pressure change depending on K, R, and w.
6m. Determine whether or not an atom should be treated as a particle or a wave.
6n. Make a sketch showing how atoms move in a Lennard-Jones potential depending on temperature, the depth of the potential, and the equilibrium distance.
6o. Describe how molecular dynamics simulations work.
6p. List what predictions molecular dynamics can make that continuum mechanics cannot.

Unit 7, A glimpse at current research (student presentations)

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

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. Should you need the complete references for these articles, please find them here . The keywords for the materials are:

Reading materials

Lab and homework materials

AFM.ShownInLecture, Things I've been showing you in class
Link to YouTube lessons, new as of D'13!

AFM.DRAFT, Draft of AFM book
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
IWGN, Nano brochure from IWGN
MDI, Molecular Dynamics I
MDII, Molecular Dynamics II
MPM, Mechanical Properties of Metals
PG, A Practical Guide to Scanning Probe Microscopy
SFA, Surface Forces and Adhesion
StiffCal, Stiffness calibration paper
StiffCalII, Another stiffness calibration paper
STM, Scanning Tunneling Microscopy

CLI, Computer Lab Instructions
Data Dlevers.pdf, Data sheet for stiff cantilevers
Data Grating, Data sheet for TGTcalibration grating
Data MPP31123, Data sheet for compliant cantilevers
EXP, Expectations of AFM Users
HW3, Homework 3
ICA, I.C.Adams manual *
ILI, Instrument Lab Instructions
ILR.docx, Template for Instrument Lab Reports (Word)
ILR.tex, Template for Instrument Lab Reports (LaTeX)
Lab5, Excel file for Lab 5 report
Lab6, Excel file for Lab 6 report
LP, Laboratory Procedures
MLI, Macro-Lab Instructions
ML1, Static spring-constant spreadsheet
No software for ML2
ML3, Dynamic spring-constant acquisition program
ML4, Cantilever-instabilities acquisition program
ML5&6, Force-curve acquisition program
SPMLab, Manual for V.5.01 *
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.

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.

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 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 Rebecca L Gaddis, rlgaddis@wpi.edu, and Gawain Thomas, gawainthomas@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.

Homework, presentation proposal, presentation abstract, and presentation

A homework assignment consists of a reading summary, two problems, and a short laboratory exercise with a macroscopic cantilever. Each will be graded out of five points. Each homework assignment contributes 2 % to your final grade. The reading summaries should be at least 200 words in length. Add a question or comment about the material or a request for me to explain something in class. Please put your questions, comments, requests, and word count at the end of your summary. Although you submit it to me, it should be written for your own benefit, so that you can use it as a study aid while preparing for the exams. Use the learning objectives above to help you pick out the important points. An example reading summary (without a question, comment, or request) is given in the reading summary section of my PH 2202 course handout. For grading guidelines for the summaries, problems, and "macro-labs", see the grading guideline section of the same page. An addition to the guidelines is that a point will be deducted if there is no question, comment, or request at the end of the summary.

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, and interest, and responses to questions.

Homework	Assignment; see above for key-word links
HW1, Fundamentals	1. Reading summary of IWGN, brochure introducing nanoscience and technology 2. State in kilometers, microns, nanometers, Angstroms, and picometers how far it is from Olin Hall to where you live. 3. Estimate the magnitude of the pressure between a coffee cup and a desk. Write the result with the correct SI unit for pressure. Estimate the magnitude of the pressure between an AFM tip and a sample if the cantilever has a spring constant of 1 N/m, it is deflected by ten times the diameter of a hydrogen atom, and the contact area with the sample is a square nanometer. What is the SI prefix for this power of ten? 4. ML1, static spring constant.
HW2, Difficulties	1. Reading summary of DraftSects2.2-3 on noise and FFTs 2. Problem 15, identifying noise 3. Problem 18, fourier coefficients 4. ML2, tip imaging
HW3, Other SPMs	HW3
HW4, Calibration	1. Reading summary of DraftSect4.1 on probe design and calibration 2. Problem 30, influence of thickness of cantilever 3. Scanner sketching exercise. Sketch the equivalent of Figs 2-5, 2-7, 2-10, and 2-11 in PG, not for a square step, but for a square well. There is a small mistake in Fig. 2-7. You should be able to puzzle out the mistake by comparing Figs. 2-6 and 2-7. 4. ML4, cantilever instabilities
HW5, Force Curves	1. Reading summary of DraftSects.5.1-2 on force-curve mechanics 2. Problem 45, instabilities for approach and retraction 3. Problem 55, taking limits 4. ML5, force curve of an infinitely stiff sample
HW6, Interactions	1. Reading summary of DraftSects.5.3 and 6.1 on materials and forces 2. Problem 60, reduced modulus 3. Problem 68, forces and charges 4. ML6, force curve of an unknown sample
PP, Presentation Proposal	Bring me hard copies of at least two related current publications that interest you about modern materials, biophysics, or nanotechnology. At least one article must be from a 2010 or later 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. 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. 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?)
PA, Presentation Abstract	The presentation abstract will reflect your understanding of the articles. It should be one page, at least 300 and fewer than 600 words in length, and submitted on paper at the beginning of class on the due date. Refer to the articles within the abstract.
PR, Presentation	Participation in the presentations, during which you will describe your articles in a short verbal presentation, is contingent upon timely submissions of a presentation proposal and an abstract.
DDD, Drop-Dead Day	All IL and EX work must be submitted before noon on 1 May 2013 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. Academic dishonestry includes intended and unintended plagiarism. The moral equivalent of academic dishonesty in larger society is treason.

Important times, places, and dates

Classes are held MTThF at 12:00.
Monday, Tuesday, and Thursday classes are in Olin Hall 223.
The fifty-minute computer labs are in Salisbury Lab 123 on Fridays.
The two-hour instrument labs are held in Olin Hall 009 Tuesday afternoons and Wednesdays.
Prelab assignments are due at the beginning of your instrument lab sessions. Other work must be submitted at the beginning of class or placed in my mailbox by noon. The exception is CL5, which is due in my mailbox by 8:00 pm on Friday, April 12th.

February 2013