PHYS 6741 Graduate Laboratory Spring 2016

Class Number: 10622

Instructor: Gang Chen, 167 Clippinger; 593-9610; cheng3@ohio.edu
Classroom: Lecture: Clippinger 133; Experiments: Clippinger 353 and 352
Day and Time: Lectures: Tue, Thu, 9 - 10:20 a.m in select weeks.
Lab sessions: 2-4 hrs total/week (Tue and Thu to be arranged)
Course Web Page: https://blackboard.ohio.edu (and choose PHYS 6741 student role)

Course Description: Selected experimental techniques used to measure structural and

physical properties of solid materials and materials surfaces as well as physical properties of
biological systems. Experimental techniques available include X-ray Diffraction, Scanning
Electron Microscopy and Laser Tweezers.

Course Objectives and Student Learning Outcomes:

Constructing knowledge collect, analyze, and interpret real data from personal
observations of the physical world to develop a physical worldview.
Modeling develop abstract representations of real systems studied in the laboratory,
understand their limitations and uncertainties, and make predictions using models.
Designing Experiments develop, engineer, and troubleshoot experiments to test
models and hypotheses within specific constraints such as cost, time, safety, and
available equipment.
Developing technical and practical laboratory skills become proficient using
common test equipment in a range of standard laboratory measurements while being
cognizant of device limitations.
Analyzing and visualizing data analyze and display data using statistical methods and
critically interpret the validity and limitations of these data and their uncertainties.
Communicating Physics present results and ideas with reasoned arguments supported
by experimental evidence and utilizing appropriate and authentic written and verbal
forms.

Required Material:
Lab Notebook: Each student must have a laboratory notebook to be used for data collection and
lab notes. You will not be allowed to begin your first experiment without a lab notebook. Leave
a few pages at the beginning of the notebook for a table of contents you can make later. If pages
of the notebook are not already numbered, you must number the pages.
Textbooks: (Chapters will be available on blackboard website)
1. Scanning Electron Microscopy and X-ray Microanalysis, Third Edition Authors: Goldstein, J.,
Newbury, D.E., Joy, D.C., Lyman, C.E., Echlin, P., Lifshin, E., Sawyer, L., Michael, J.R.
2. Fundamentals of Powder Diffraction and Structural Characterization of Materials, Authors:
Vitalij K. Pecharsky, Peter Y. Zavalij
3. Underneath the Bragg Peaks: Structural Analysis of Complex Materials, Authors: Takeshi
Egami, Simon Billinge
4. Methods of X-ray and Neutron Scattering in Polymer Science, Author: Ryong-Joon Roe

Course Activities:
You will do five groups of 1-2 week experiments (see schedule) plus one final project using the
equipment in the list below:
Equipment Currently Available:
1. Scanning Electron Microscope (SEM) (2 weeks)
2. Energy Dispersive X-ray Spectroscopy (EDXS) (2 weeks)
3. X-Ray Diffraction(XRD) (2 weeks)
4. Pair Distribution Function (PDF) (1 week)
5. Optical video microscopy and optical trapping (OT) of biological samples (1 week);
OR
Small-angle X-ray Scattering (SAXS) (1 week)
Materials Currently Available:
1. Crystalline or amorphous thin film samples
2. Metal samples (coins are and other metal alloys)
3. Powder samples (can be purchased, some old ones exist already)
4. Latex microspheres for OT experiments
Students are encouraged to bring their own samples that fit in the purpose of the lab.
Each experiment will be performed and written up over a two week cycle. One to two weeks will
be spent collecting data. The second/third week will be reserved for finalizing the lab writeups
and performing any last minute experiments that analysis has suggested are necessary for
confirmation.
The final lab writeup (in poster and paper form) will be due (in electronic form on
Blackboard) by 5:00 p.m. on Thursdays of one week after the scheduled lab is completed.

Lab Notebook
Each student must purchase a lab notebook to record results of experiments. Data-taking records
must be found in each persons lab notebook. If one person of a team is responsible for taking
notes or data, records of that data must be also found in the other team members notebook.
Credit will not be given to one person based on his/her lab partners notebook.
Keeping a good notebook is critical for recording the data you have taken as well as the methods
you have followed and any special circumstances or deviations from established protocols that
occurred. Each persons notebook should be a complete record of the experiment. If you use a
computer for recording data, you must print out records and paste them into your lab book. The
lab book is an ongoing, up-to-date journal/record of your experiment. Your lab book is to be a
good enough record so that someone can pick it up and figure out what you did, including what
might have gone wrong.
Lab notes are due in class on Thursdays of one week after the scheduled lab is completed.
Criteria for grading the lab notebook:
Table of contents and page numbering (organization) 25
Comprehensibility (i.e. how easy is it to follow)
25
Completeness (i.e. is everything there)
25
Reasonableness of data and explanations of data
25
Total
100

Reports:
You will turn in a report for each of the four experiments plus the final project. These will be
presented in the three most common forms used for scientific communication:
1) Paper: A paper is the most detailed (and prestigious) form of scientific communication. All
papers have the same basic set of sections. You are required to follow the Physical Review
format.
a) Title page: This should have title, author, and authors affiliation.
b) abstract: This will be the (revised) abstract submitted the week before the paper is due.
c) Introduction: This should give background about the study that has been done and some
motivation or reason for why anyone should care about the work. It is often desirable to have
an underlying hypothesis (or burning question) that is to be demonstrated (although this is not an
absolute requirement for more investigation driven experiments). The hypothesis should be
described in the introduction.
d) Materials and Methods: In labeled sections, the materials used and the equipment should be
described. The methods used, descriptions of statistical techniques and of sources of systematic
and random errors should also appear here.
e) Results: This section should be built around numbered figures (graphs, images, diagrams) and
tables. This section must also have a significant amount of text that describes all of these figures
in sufficient detail that one could determine which figure or data table is being described without
needing the figure or table number. It is not enough to just give a bunch of figures and tables
without a logical description of what they show.
f) Discussion: What the results mean should be explained. The last few paragraphs should sum
up the work and give the final conclusions (sometimes this is done in a Conclusions section).
g) References: The sources for non-obvious statements and any quoted material should be listed
in a References section at the end. These sources could be books, papers, webpages or some
other medium. When in doubt about whether a reference is necessary, err on the side of including
one since otherwise one could be accused of plagiarism (see Misconduct segment below).
2) Poster: The poster is a common form of presentation for scientific meetings. Nowadays, the
cost of printing a poster has decreased to the point that large one-panel posters dominate. At
Ohio University, posters can be printed by Printing Services and by various other smaller outfits
around the University. Posters will be prepared using 36 x 48 Powerpoint poster templates
(available for download at the course website). The same sections should be present as for a
paper (Header with name and affiliation, abstract, introduction, materials and methods, results,
discussion, references). Here, however, the emphasis is on clear, logical and attractive
presentation with figures, tables and diagrams dominating and descriptive information given in
short captions or bulleted lists of major points. It is important in a poster to have a separate
Conclusions section that summarizes the results of the paper. Make sure that the text size is large
enough to be read at some distance from the poster. You will submit (via Blackboad), the
completed Powerpoint poster templates.
3) Webpage: Webpages are increasingly used for communication of scientific results. The same
sections should be present as in a poster: (abstract, introduction, materials and methods, results,
discussion, conclusion, references), however, some of these could be on a main webpage with
the title and header information and others could be hyperlinks. As with a poster, conciseness
and attractiveness are important for front pages, but links can also be given to more detailed
analyses and to external sources. Web pages can be prepared using HTML tags using any text
3

editor. Microsoft Word documents can be saved as HTML (although this generally creates badly
cluttered HTML). There are free, open source WYSIWYG HTML editors (e.g. Nvu, Mozilla
Composer, Seamonkey) that can be downloaded and used. You may also be able to find old
copies of Microsoft Frontpage (that used to be part of Microsoft Office).

Criteria for grading of reports:

Appearance, comprehensibility and logical organization
Completeness
Reasonableness
Creativity and originality
Total

30
30
30
10
100

Grades
Paper
Poster
Web page
Participation
Lab notebook
Total

45%
20%
10%
5%
20%
100%

A tentative guide for final grades is:

85 100
A
70 85
B
60 70
C
50 59
D
59 0
F

Academic Honesty and Plagiarism:

We are required to remind you that cheating and plagiarism are considered very serious
violations of the Code of Student Conduct. In particular, submissions that are identical or very
similar to those of other students could result in an accusation of plagiarism. Further, copying
from sources (or copying with minor modifications) is plagiarism unless the copied material is
indicated (using quotation marks) and proper attribution is given. This subject will be discussed
further in class.
Students caught in flagrant cheating may be given a zero on the class work involved or be asked
to resubmit the work. If the student does not agree with this action, the student may file a
grievance through established University channels or through the Ombudsman's office. In
extreme cases the instructor may also initiate a review by the University Judicial Board. This
action could result in suspension of the student or other punitive actions by the Judicial Board.
All cases involving flagrant cheating or suspected cheating will be reported to the Chairman of
the Department of Physics and Astronomy in writing for future reference.
The blackboard is equipped with plagiarism checker.

Preliminary Schedule (Subject to change):

Week Dates
LAB
Note
1 Jan 12 Lecture Introduction/ Error Analysis
14 Lecture Error Analysis/SEM
2
19 Lecture SEM
21 Lecture SEM
3
26
SEM Basic SEM Imaging
28
SEM Basic SEM Imaging
4 Feb 2
SEM Image Contrast and Quality
4
SEM Image Contrast and Quality
5
9
Lecture EDXS
11 Lecture EDXS
6
16 EDXS Energy-Dispersive X-Ray
Spectrometry
18 EDXS Energy-Dispersive X-Ray
Spectrometry
7
23 EDXS Energy-Dispersive X-Ray
Microanalysis
25 EDXS Energy-Dispersive X-Ray
Microanalysis
8 Mar 1
Spring Break
3
Spring Break
9
8 Lecture XRD
10 Lecture XRD
10
15 Lecture XRD/PDF
17 XRD Powder Diffraction
11
22 XRD Powder Diffraction
24 XRD Indexing and Identification
12
29 XRD/ Indexing and Identification/
PDF Pair Distribution Function
31
PDF Pair Distribution Function
13 Apr 5 Lecture OT/SAXS
7 Lecture OT/SAXS
14 .
12 OT or Optical Trapping/
SAXS Small Angle X-ray Scattering
14 OT or Optical Trapping/
SAXS Small Angle X-ray Scattering
15
19 Final Comprehensive Project
Project
21 Final Comprehensive Project
Project
Final
28 Final Comprehensive Project
Project
Project

Due

Lab notes, paper of SEM due

Lab notes, paper of EDXS due

Lab notes, papers of XRD/PDF due

Lab notes, web page of OT/SAXS due

Final project poster due

Group Assignment

Group 1

Group 2

Group 3