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How to Complete the Thesis Requirement
for students in fields using AIP/LaTeX styles*
In this packet, you will find the following:
1. Guidelines for preparing the thesis proposal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Theses and capstone projects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
How to begin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
How to write the proposal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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2. Deadlines for completing steps in the thesis requirement . . . . . . . . . . . . . . . . . . . . . . . . 5
3. Sample proposal for your field or a related one . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
4. Form 4, Thesis Proposal Submission Form . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
5. Form 5, Application for Undergraduate Research Funds . . . . . . . . . . . . . . . . . . . . . . . 15
6. Instructions for writing the thesis and scheduling the defense . . . . . . . . . . . . . . . . . . . 16
7. Form 6, Thesis Submission Form . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
8. Instructions for preparing the final copy of the thesis . . . . . . . . . . . . . . . . . . . . . . . . . . 18
9. Format requirements for all theses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
10. Sample pages from a thesis in your field or a related one . . . . . . . . . . . . . . . . . . . . . . 22
*Recommended for students majoring in physics, math, and other sciences that use formulae.
Manuscripts in the physical and engineering sciences will include a great many technicalities, too
numerous to illustrate here. Please consult with your advisor concerning formatting specifications
for publications in your field. If no specific recommendations are made, you may follow the
format patterns presented here.
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Guidelines for Preparing the Thesis Proposal
Theses and Capstone Projects
There are two ways to complete the thesis requirement for Honors. One is to write the traditional
thesis; the other is to complete a capstone project. Preparing a thesis or capstone project is a way
for you to demonstrate that you possess sufficient knowledge of the learning and methods of your
discipline to create an original contribution, however small, to your field. Whether you choose to
do a thesis or a capstone project depends largely on your major and your interests.
The Thesis
A thesis is the most appropriate way to end a degree program in theoretical, historical, and
scientific disciplines for which the end product of research or creative exploration is usually
a text. For example, in art history, botany, chemistry, economics, English, French, history,
philosophy, psychology, sociology, or zoology, a practitioner would write a text that
presents the results of research done in the library, the laboratory, or the field. Essentially,
the thesis is a presentation and interpretation of the research results.
The Capstone Project with accompanying documentation
A capstone project is the most appropriate way to end a degree program in certain
specialized disciplines for which the end product of research or creative exploration is
usually a performance, exhibit, or object that you create. For example, in art, engineering,
computer science, dance, education, music, or creative writing, a practitioner typically
would create something for others to enjoy (such as an exhibit of paintings, a dance, a
musical performance, or a short story) or to use (such as a software program, a medical
device, or pedagogical materials). If you are majoring in one of these disciplines or a
similar one, a capstone project is an acceptable alternative to a thesis. However, the
performance or product you create should be aimed at a broader audience than BYU; it
should have more than local applicability. In addition, you must document the experience
of creating your project by writing a text that contains the following parts:
•
•
•
•
•
•
the purpose of the project,
why the project was a suitable culminating experience for your education,
the procedures or methods you used to create the project,
a log of the hours you spent,
accompanying texts, sketches, diagrams, photos, or audiotape/videotape that help
document the project,
signature of the professor who supervised the project and can attest to its quality.
Although these two ways of completing the thesis requirement differ, for convenience both will be
referred to simply as a thesis. Completing either successfully depends on starting well.
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How to Begin
Completing a thesis is a long process that will stretch over at least two semesters. Planning your
thesis is of great importance and always includes at least the first three of the following four steps:
Step 1. Schedule a thesis orientation meeting. Go to 350 MSRB and ask for an
appointment to discuss your thesis plans with the Associate Dean of Honors and General
Education who supervises theses. The orientation meeting will help you (1) choose a thesis
topic; (2) choose a thesis advisor; and (3) obtain funding, if you need it.
Step 2. Choose a thesis advisor and narrow your topic to a manageable scope.
During or after your thesis orientation meeting, you must choose a professor to direct the
writing of your thesis or the completion of your project and a second professor to be the
referee. Normally, they will be professors in your major or a closely related field. The
advisor should be a full-time faculty member with a continuing appointment at BYU, not a
part-time instructor or visiting professor.
As you seek an advisor, it is best to start with a broad general interest rather than a specific
topic for your thesis. Next, find out which faculty have expertise in the area of your general
interest. (You’ll waste time if you focus on a narrow topic too soon only to learn there are
no faculty on campus who have the expertise to advise you. It’s better if you make your
project match faculty expertise rather than vice versa.) Then talk to these experts and let
them help you focus on a specific topic that they are qualified to advise you about. Often in
the sciences, a professor will assign you a research project to do that is part of a larger
project the professor is engaged in.
Step 3. Write a proposal for your thesis.
Once you have chosen a topic and advisor, let your advisor and referee guide you in writing
the proposal so that you can define a workable focus and scope for your thesis and establish
a reasonable time line for completing it by established deadlines. (See proposal guidelines
below; pay special attention to the deadlines on page 5.)
Step 4. Obtain funding for your research, if necessary.
If you need funding for your thesis, fill out and submit the Application for Undergraduate
Research Funds (Form 5 in this packet). You should also consider submitting an
application for a research scholarship offered by the Office for Research and Creative
Activities (ORCA) in A-261 ASB. This scholarship consists of a $1,000 unrestricted grant.
The deadline for submitting proposals for an ORCA scholarship is usually the middle of
October.
How to Write the Proposal
Whether you write a thesis or do a capstone project, you must first write a proposal to be approved
by (1) your thesis advisor, (2) the Honors Coordinator in your department, and (3) the dean or
associate dean of the Honors Program, or a person designated by Honors to review the proposal.
How you write the proposal will depend on what you have chosen to do. But in general, your
proposal should be about 5 or 6 double-spaced pages and should have the following parts:
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I. Purpose. In this section of the proposal tell what you aim to do. If you plan to conduct scientific
research, state the hypothesis you will test, the problem you will solve, or the research question(s)
you will answer. If you are planning a non-science thesis, state the question(s) you want to answer
or the claim you plan to argue for. If you are planning a capstone project, tell what it will include.
II. Background and Significance. In this section, explain the context of your proposed research.
The context might be historical, social, cultural, political, and/or personal. Usually, a context is
created by a brief review of related literature on your topic. This means that before you write your
proposal, you will have to do library research to learn what others have already written about the
question, problem, or topic your thesis will address. After establishing the background of your
research, tell why the thesis or project should be done. You can do this by showing how your
proposed work will add to, differ from, or relate to the work previously done.
III. Methods or Procedures. What you include in this section will depend on what sort of
research you plan to do. Regardless of the type, you should spell out the steps you will take to
complete the thesis research or produce the objects or performance required for a capstone project.
Here are three lists of possible items to include in this section, depending on the type of thesis or
project you do:
Scientific Thesis
Materials
Instruments
Procedures
Participants
Data Analysis
Non-scientific Thesis
Texts to be used
Theories to be applied
Models to be followed
Analytical tools to be used
Categories of information sought
Capstone Project
Rehearsal schedule
Production processes and schedule
Needs assessment
Usability tests
Quality control procedures
Please note that you must also obtain permission from the BYU Institutional Review Board
(IRB) if you plan to do research that will involve human participants. For example, research
methods that involve surveys, interviews, controlled observations, or experiments with human
participants must be approved by the IRB or its representatives to ensure that participants are able
to give their informed consent and will not suffer any harm or violations of their rights as a result
of participating in your research. Getting IRB approval is not difficult if the research is well
planned. However, it can add a month or more to the time needed to have your thesis or project
proposal approved. To learn more about IRB requirements and the approval process, contact the
Associate Director for Compliance in the office of Research and Creative Activities in A-261 ASB
(378-3841).
IV. Prospectus of Finished Text. In this section, provide a tentative outline of what your thesis or
the documentation of your project will include. If you are writing a scientific thesis, it is very likely
that the outline of your final text will simply be Introduction, Methods, Results, and Discussion. If
you are writing a non-scientific thesis, try to project the main divisions of your argument and show
how your thesis will be organized. If you are documenting a capstone project, outline the contents
of the narrative you will write to document what you did, including the purpose of the project, how
it crowned your education, the process you went through, and the hours spent. (This narrative may
be accompanied by sketches, diagrams, photos, or possibly even a videotape or audiotape to record
the performance, the display, or the object created.)
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V. Preliminary Bibliography. In this section, list the books, articles, and other sources you have
read to review the literature related to your research. Use the documentation style that is standard
for your discipline.
VI. Qualifications of the Investigator. In this section, describe the courses you have taken and
experiences you have had that qualify you to undertake the research or the project you are
proposing. If your thesis or project requires particular skills with statistics, mathematics, foreign
languages, computers, etc., be sure to explain that you possess the required skills and knowledge.
VII. Qualifications of the Advisor. In this section, name your faculty advisor and describe his or
her qualifications. In most cases, your advisor should be a professor who publishes in your area of
interest, if you are writing a thesis. If you are doing a capstone project, it should be a professor who
performs or creates art or products of the type you want to produce.
VIII. Time line for completing your thesis or capstone project. In this section of your
proposal, list the sub-tasks that will be required to complete your thesis and a date by which you
will complete each sub-task so that you meet the Honors Program deadlines in the table below.
IX. Budget (if needed). In this section, list all expenses (supplies, services, travel, etc.) required
for your research or project and the dollar amount for each expense. Add the amounts of the line
items for a total. If you have not already submitted Form 5, submit it with your proposal.
Deadlines for Completing the Thesis for Graduation with University Honors
For graduation in
April
August
December
Thesis proposal approved by
May 15
September 15
January 15
First draft of thesis submitted to advisor
and referee by
November 15
March 15
July 15
Final draft of thesis and portfolio
submitted to Honors Program by
February 1
June 1
October 1
Thesis defense scheduled by
February 5
June 5
October 5
Thesis defense completed by
March 1
July 1
November 1
Four final copies of thesis submitted to
Honors Program by
March 15
July 15
November 15
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SAMPLE THESIS PROPOSAL
A Three-Barrier, Two-Site Analysis of Gramicidin Conductivity
in Fluorinated and Native Peptides
by Nephi Thompson
I. Purpose
For my honors thesis project, I propose to utilize an enhanced 3B2S model to compare
energy profile differences between fluorinated and non-fluorinated gramicidin channels. Through
this analysis, I hope to further elucidate the effect of fluorination on gramicidin function. To carry
out this analysis, I will write and execute the computer programs needed to analyze and compare
the closeness of the fit between the model and the data. These programs include a 3B2S model
that will calculate currents given an energy profile, and a non-linear least squares fit that will
compare predictions from the model program to measured data and will iterate toward minima. In
my thesis, I will discuss the success of my analysis and its relevance to membrane biophysics.
II. Background and Significance
Ionic channels span cell membranes and allow specific ions to pass into or out of a cell.
They operate in each of our body’s cells to maintain the proper physiological gradient of ions.
Notable examples of cells that have specific ion gradient requirements are neurons and muscle
cells. When ionic channels malfunction and disrupt the necessary gradients, cell function is greatly
inhibited, leading to trauma and possibly death [1].
Since the discovery of ionic channels, many researchers have sought to better understand
them. Furthering the study of the properties and characteristics of ionic channels, Paul Mueller and
Donald Rudin developed practical ways to make lipid bilayers, which are the major component of
cell membranes. They developed a method to form bilayers of pure lipids or lipids mixed with
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inert solvents such as decane across a small hole in a Teflon or plastic barrier separating two
compartments. The compartments could then be filled with different solutions and the voltage
across the bilayer clamped to study the ionic permeability of the bilayer [2; 3]. Later researchers
introduced channel-forming substances into these bilayers and measured their effect on ionic
permeability over a range of voltages and concentrations for a variety of ions.
One of the most commonly used channel-forming substances is gramicidin A, a peptide that
forms transmembrane channels that are selective for monovalent cations. Gramicidin A is
produced by various strains of Bacillus brevis and is used as an antibiotic [4]. A linear peptide
with known primary sequence (Val, Gly, Ala, D-Leu, Ala, D-Val, Val, D-Val, Trp. D-Leu, Trp. DLeu, Trp, D-Leu, Trp), gramicidin A is the only small ion pore whose primary amino acid sequence
is completely known. The side chains are all hydrophobic; thus the peptide can be easily inserted
into lipid bilayers. With only 15 amino acids, it is the simplest and best characterized channelforming peptide [5].
Kinetic and chemical experiments show that the channel consists of two gramicidin
peptides transiently dimerized head-to-head by hydrogen bonds. The secondary structure of the
peptide is a right-handed helix with a central pore stabilized by --NH- - -O-- hydrogen bonds that
extend parallel to the pore between groups six residues apart. The channel forms as the two helices
dimerize as discussed, and it has a central pore of 4 in diameter and is about 25 long [6; 7].
Since the discovery of ionic channels, models of ion transport have been developed to
describe their energetics, mechanics and kinetics. The movement of ions through the channel can
be considered as an electrodiffusion problem and can be modeled using Nernst-Plank continuum
theory, Brownian dynamics or Eyring rate theory [5]. Thus far, Eyring rate theory has proved the
most expedient and appropriate, especially with recent developments and enhancements [8].
However, Nernst-Plank and Brownian dynamics methods are still being developed, most notably
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by David Leavitt [9] and Erik Jakobsson [10]. This review will treat Eyring rate theory and leave
the other models to the reader’s further exploration.
Eyring rate theory describes electrodiffusion as hopping over energy barriers. The hopping
model replaces the continuous diffusion profile by a corrugated energy profile and the diffusion
equation by rate equations. The rate constants are exponentially related to the height of the energy
barriers by absolute reaction rate theory, developed by Henry Eyring [11; 12]. Generally, Eyring
rate models describe ion movement through the channel as a series of three steps: ion diffusion up
to the entry of the channel and binding to the entry site, translocation through the channel to the
exit site, and release from the exit site and diffusion away from the channel.
The earliest application of Eyring rate theory to channel kinetics was by Hodgkin and
Keynes, who used barrier models to explain their potassium permeability results in squid axons
[13]. General theoretical models using saturating barrier one-ion channels were developed by
Heckmann [14] and Lauger [15] while Hladky introduced a model for gramicidin that had three
energy barriers and two ion binding sites [16].
These early researchers noticed concentration-dependent permeability ratios and deviations
from the Ussing [17] flux-ratio test which implied that a one-ion model would be inadequate.
Hladky [16] and Lauger [15] reported concentration-dependent shapes of gramicidin currentvoltage plots; at low ion concentrations the plot was concave toward the voltage axis (“sublinear”),
while at high ion concentrations the plot was convex (“supralinear”). This concentration
dependence implied that the channel would best be modeled with multiple barriers. Also, the fluxratio exponent observed experimentally for gramicidin channels was greater than 1.0, which
implied that there were multiple ions in the channel [18].
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Due to these experimental concerns, researchers sought for a suitable multiple barrier,
multiple ion, Eyring rate model for gramicidin conductance. Further research, which showed that
the channel was single-filing with ions and water molecules unable to pass each other due to the
narrowness of the pore, simplified the formulation of a suitable model [19; 20]. The three-barrier,
two-site, single-filing double occupancy model (3B2S) first proposed and developed by Hladky to
describe gramicidin conductance [21; 22] has proven adequate in describing most of the
conductance features of the channel and has gained acceptance in the field as a valid model.
Furthermore, NMR studies [23] and X-ray diffraction studies [24] have demonstrated two
symmetrical binding sites in the gramicidin channel, giving a physical justification for a 3B2S
model.
Since its development, a number of modifications have been suggested to improve the
3B2S model. It has been enhanced in the three-barrier, four-site model, which depicts entry and
exit from the channel as a compound step [25]. An enhancement presented by Olaf Andersen takes
two effects of the external solution, the diffusion limitations and the interfacial polarization, into
account when calculating conductance [26]. Hladky also studied the roles of diffusion and other
external access steps and proposed enhancements [27]. Urry and colleagues have also used NMR
to calculate the first and second ion-binding affinities and entry and exit rate constants which help
to characterize the energy profile of the channel [28]. And finally, Roux and colleagues have used
free energy computations to calculate the energy barriers for ion passage through the channel [29].
With these modifications, the three-barrier, two-site model (3B2S) has been successful in
predicting most of the features of ion conductance data in gramicidin channels.
Using gramicidin peptides, Dr. Busath’s lab at Brigham Young University has collected a
large body of data that consists of currents measured at various concentrations, voltages and
temperatures. This conductivity data is then analyzed for precision and a statistical confidence
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value is calculated. Dr. Busath and associates have taken data using fluorinated and native (nonfluorinated) gramicidin peptides in an attempt to study the effect of fluorination on the conductivity
of the channel. This course of research appears fruitful because the addition of fluorine appears to
change the electrical profile of the channel by modulating the interaction of ions with the peptide.
Analysis of this data will hopefully elucidate the specific effect of fluorine and will lead to a better
understanding of the electrical profile of the channel and its interactions with ions.
I feel that this thesis project will advance 3B2S modeling and will be of value to other
membrane biophysicists. Besides writing my thesis, I will also submit my findings to the
Biophysical Journal for publication.
References (only the first five are included here)
[1]
Bruce Alberts, Dennis Bray, Julian Lewis, Martin Raff, Keith Roberts, and James D.
Watson, Molecular Biology of the Cell, 3rd ed., New York, Garland Publishing, Inc., 1994.
[2]
P. Mueller, D.O. Rudin, H.T. Tien and W.C. Wescott, "Reconstitution of cell membrane
structure in vitro and its transformation into an excitable system," Nature, 194, 1962, pp.
979-980.
[3]
P. Mueller and D.O. Rudin, "Translocators in biomolecular lipid membranes: Their role in
dissipative and conservative bioenergy transductions," Curr. Topics in Bioeng, 3, 1969, pp.
157-249.
[4]
William M. O'Leary, ed. Practical Handbook of Microbiology, Boca Raton, CRC Press,
Inc., 1989.
[5]
B. Hille, Ionic Channels of Excitable Membranes, Sunderland, Mass., Sinauer Associates,
1984.
. . . and so on
III. Methods
To complete the project, I propose to do the following:
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1. Review the literature for other attempts at energy barrier modeling.
2. Write the program that will calculate the current through the channel given the energy
profile of the channel from the model.
3. Write the procedure that will analyze the fit between the model and the data and that
will vary the parameters according to a nonlinear least squares algorithm until model
and data reach an optimal fit.
4. Using the optimal fit obtained, compare the results to other data (NMR, X-ray
crystallography, tracer flux, etc.)
5. Analyze the optimal fit energy profile to find relationships between parameters.
6. Report the results of my analysis in my honors thesis.
IV. Prospectus of Finished Text
My thesis will be formatted like a journal article, because I hope to publish it as one.
A.
B.
C.
D.
E.
F.
Abstract
Introduction
Computational Procedures (Methods)
Results
Discussion
References
V. Preliminary Bibliography
Bruce Alberts, Dennis Bray, Julian Lewis, Martin Raff, Keith Roberts, and James D. Watson,
Molecular Biology of the Cell, 3rd ed., New York: Garland Publishing, Inc., 1994.
O.S. Anderson, D. Greathouse, L.L. Providence, M.D. Becker, and R.E. Koeppe II, "Importance of
tryptophan dipoles for protein function: 5-Fluorination of tryptophans in gramicidin A
channels," J. Amer. Chem. Soc., 120, 1998, pp. 5142-5146.
D. Busath and G. Szabo, "Permeation characteristics of gramicidin conformers," Biophys. J., 53,
1988B, pp. 697-707.
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H. Eyring, "The activated complex in chemical reactions," J. Chem. Phys., 3, 1935, pp. 107-115.
B. Hille, "Ionic Channels of Excitable Membranes," Sunderland, Mass, Sinauer Associates, 1984.
P.C. Jordan,"The total electrostatic potential in a gramicidin channel," J. Membr. Biol., 78, 1984,
pp. 91-102.
P. Mueller and D.O. Rudin, "Translocators in biomolecular lipid membranes: Their role in
dissipative and conservative bioenergy transductions," Curr. Top. Bioeng. 3, 1969, pp.
157-249.
P. Mueller, D.O. Rudin, H.T. Tien and W.C. Wescott, "Reconstitution of cell membrane structure
in vitro and its transformation into an excitable system," Nature 194, 1962, pp. 979-980.
William M. O'Leary, ed., Practical Handbook of Microbiology, Boca Raton, CRC Press, Inc.,
1989.
D. W. Urry, K.U. Prasad, T.L. Trapane, "Location of monovalent cation binding sites in the
gramicidin channel." Proc. Natl. Acad. Sci., 79, 1982, pp. 390-94.
VI. Qualifications of the Investigator
The classes I have taken in introductory physics and those I have taken for my math minor
have prepared me for this research. These classes include Linear Algebra, Multivariable Calculus,
Ordinary Differential Equations, and Partial Differential Equations; Physics 121, 122, 221, 222—
a series covering mechanics, electricity and magnetism, optics, thermodynamics, relativity and
quantum mechanics; Intro to Biology, Molecular Biology; and several upper-division courses in
physics, chemistry, and zoology.
I have also completed a review of the history and literature of this area of scientific study;
my research is summarized in this proposal.
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VII. Qualifications of the advisor
I have selected Dr. Busath because his of research in ionic channel fluxes, conductivity, and
modeling in the biophysical realm. He has many years experience with measuring and modeling
gramicidin channel characteristics. He is excited to work with me because he has always wanted to
have this analysis performed on his data, but has never had the time to write and implement it,
owing to his other faculty and research responsibilities.
VIII. Time line for completing thesis
9 Apr 1999
15 Apr 1999
1 May 1999
1 Aug 1999
15 Aug 1999
1 Sep 1999
15 Sep 1999
1 Oct 1999
IX.
Submit thesis proposal
Finish thesis introduction and literature review
Model and analyze collected data
Finalize all fits, graphs, and figures
Begin discussion section of thesis
Have first rough draft of complete thesis
Have polished draft of thesis
Complete writing and revising thesis
Budget
I hope that I will be able to do this research as my part-time job. I have requested the
following funding to pay for 200 hours of work at $10/hr:
$500 from Honors
$500 from Physics
$1000 from Zoology
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HONORS PROGRAM
BYU
THESIS PROPOSAL SUBMISSION FORM
Name
BYU ID Number
Local Address
Local Telephone
City
State
Permanent Mailing Address
Permanent Telephone
City
State
Submission Date
Semester of Graduation
Major(s)
Minor(s)
Zip
Zip
Thesis Title
Please print or type the following information:
Faculty Advisor
Office
Telephone
Faculty Referee
Office
Telephone
Honors Coordinator
Office
Telephone
Please obtain the following signatures:
Faculty Advisor
Date
Honors Coordinator
Date
To be answered by the Honors Coordinator in consultation with the Advisor:
$
$
$
$
Do the proposed scope and contents of the thesis meet the standards expected of an Honors student?
Are the methods the student will use clearly explained and is he/she capable of using the methods?
Are the methods appropriate to answer the research questions?
Does the student have IRB approval if required (approval must be obtained before submission)?
Q Yes
Q Yes
Q Yes
Q Yes
Q No
Q No
Q No
Q No
For office use only
Honors Approval
Date
Comments
Funding requested? Q Yes
Q No
Last Revised: June 10, 2004
102A MSRB Provo, Utah 84602 · (801) 422-5497 · [email protected] · www.byu.edu/honors
HONORS PROGRAM
BYU
APPLICATION FOR UNDERGRADUATE RESEARCH FUNDS
Name
BYU ID Number
Local Address
Local Telephone
City
State
Submission Date
Semester of Graduation
Major Department
College
Zip
Thesis Title
Have you requested funding from your department for your thesis project?
Q Yes Q No
Have you applied for an ORCA (Office of Research and Creative Activities) grant?
Q Yes Q No
Proposed funding period will begin and end
Month/Year
Month/Year
In what form(s) will the results of your research be reported?
Describe briefly the relationship of the proposed funding to the thesis. Include an itemized budget. Attach additional
information, if necessary.
Advisor’s Signature
Date
Student’s Signature
Date
For office use only
Honors Recommendation (other sources of funding?)
Honors Approval
Date
Amount of Funding
Last Revised: January 23, 2004
102A MSRB Provo, Utah 84602 · (801) 422-5497 · [email protected] · www.byu.edu/honors
Instructions for Writing the Thesis and Scheduling the Defense
After your proposal has been approved by your advisor, department honors coordinator, and a
representative of the Honors Program, you are ready to begin carrying out your research and
writing your thesis. Here are the steps to follow:
Step 1. Conduct your research or complete your capstone project. Normally, you will do the
research or the preparation for your project the semester before you write the thesis or
accompanying documentation. Work closely with your advisor throughout the research phase to
be sure you are gathering the right data or information. Keep a careful log of your research efforts
and take notes about information that will likely become a part of the final document.
Step 2. Write a first draft and as many intermediate drafts as your advisor requires. Show
your draft in stages to your advisor as you complete each part. The advisor and, in most cases,
the referee should see a complete first draft about two months before you plan to have your
defense. Subsequent drafts are almost always necessary before you write a final draft. Do not
expect to write and submit only one draft of your thesis, then hold your defense a few days later.
Refer to the table on page 5 to remind yourself of deadlines you must meet.
Step 3. Write a final draft. The final draft will be read by your advisor, referee, and a
representative of the Honors Program prior to your thesis defense. The final draft should conform
to the Honors Program’s specifications for the final copy that is bound and submitted to the
library. These specifications are explained and illustrated on the final pages of this packet. Since
additional changes in the thesis may be necessary after the defense, the final draft may be printed
on regular paper. Not less than one week prior to your defense, give your advisor and referee a
copy of the final draft, and have your advisor sign Form 6, the Thesis Submission form. Bring a
copy of the final draft to 102A MSRB for the Honors Program representative who will chair your
defense. Form 6 should be attached to the Honors Program copy.
Step 4. Schedule your thesis defense. When your final draft is nearly ready, contact the Honors
Advisement Center in 102A MSRB to find out who will chair your defense. Contact the chair,
your advisor, and your referee to schedule a time (at least one hour) when all three can meet for
the defense. It is also your responsibility to find a room for the defense. The department secretary
in your major department can usually help you schedule a room; the Dean’s secretaries in 302
MSRB can also tell you about the availability of the Honors conference room. At your defense
the three readers of your thesis will ask you questions about your research and the claims that you
make in your thesis. Remember that you must complete the defense by the specified deadline in a
given semester to be eligible for graduation with University Honors. Please refer to page 5 of this
packet for the deadline you must meet.
16
HONORS PROGRAM
BYU
THESIS SUBMISSION FORM
Name
BYU ID Number
Submission Date
Semester of Graduation
Major(s)
Minor(s)
Thesis Title
Place
Tentative Date of Thesis Defense
Time
Faculty Advisor
Faculty Referee
Approximate hours spent on thesis:
Research
Writing
The thesis will be submitted to the following for publication (not required):
I hereby submit my work for approval to meet the Honors thesis requirement for graduation with University Honors.
Student’s Signature
As the thesis advisor, I certify that the attached thesis is ready to defend.
Advisor’s Signature
For office use only—to be completed at the thesis defense
Honors Representative
Actual Date of Thesis Defense
Recommendation of Committee
Place
Q Pass
Q Pass with Qualification
Time
Q Recess
Is there anything particularly noteworthy about this thesis? (cite particulars)
This form must be returned to 102A MSRB by a member of the committee after the defense;
it should not be given to the student.
Last Revised: January 12, 2004
102A MSRB Provo, Utah 84602 · (801) 422-5497 · [email protected] · www.byu.edu/honors
Instructions for Preparing the Final Copy of the Thesis
When you have passed your defense, the following steps will be necessary to complete the thesis
requirement:
Step 1. Correct and format your thesis. Make the final corrections in your thesis required by your
thesis defense committee. Then format your thesis for printing. The next two pages outline the format
that all theses must conform to. The pages at the end of this packet illustrate and explain format
conventions that are peculiar to your discipline. Each of the model pages shows how to format a
particular part of the thesis and what to include in it. The small red type in the left hand margin
explains the details and the reasoning behind the format conventions.
Step 2. Submit four unbound copies to the Honors Program. After you have formatted your thesis,
prepare four unbound copies on acid free bond paper to submit to the Honors Program Office in 102A
MSRB. Before submitting the copies, however, you must obtain the signature of
your advisor and honors representative on all four copies of the title/signature page.
18
Format Requirements for All Theses
Margins and Fonts
Observe these guidelines:
1. Leave a margin of one and one-half inches on the left side of each page to allow for
binding.
2. Leave one-inch margins on the top, bottom, and right side of each page.
3. Unless your advisor and style guide require it, do not justify the right margin;
doing so makes the text more difficult to read.
4. Use at least a 12-point font for the body of the thesis (footnotes and captions for
tables and figures can be set in a smaller font.)
5. Use a serif font for the text of the paper; research shows it is easier to read.
6. You may use a sans serif font for titles and headings, if desired.
This is an example of a serif font.
This is an example of a sans serif font.
Front matter
The following pages should come before the text of the thesis in the order indicated.
1. Title/signature page
2. Acknowledgments page, if desired
3. Table of Contents
4. List of Tables and Figures, if any have been used in the thesis
5. Abstract (summary) of the thesis
Body of the thesis
Please observe the following conventions in organizing the body of the thesis.
1. Divide the body of the thesis into sections or chapters as indicated in the Table of
Contents.
2. Give each section or chapter a heading that corresponds to headings used in the
Table of Contents.
4. Number all pages of the body of the thesis sequentially with Arabic numerals.
5. Number tables, if any, sequentially, e.g., Table 1, Table 2, etc.
6. Number figures, if used, sequentially, e.g., Figure 1, Figure 2, etc. Figures include
drawings, graphs, photos, diagrams, maps–anything that is not a table.
7. Give each table or figure a descriptive caption that explains clearly what is presented
in the table or figure.
8. Place tables and figures close to the relevant text, but not before a reader needs them.
19
Back Matter
All theses will have the first of these, and many will have the second.
1. References, Selected Bibliography, Works Cited, or Works Consulted. The title you
use will depend on the documentation style you have followed. These pages must
contain full bibliographic citations for all documents, printed or electronic, you have
consulted and cited in the thesis.
2. Appendix(es). Place in an appendix raw data (e.g., calculations, transcripts,
tabulations, matrices, etc.) which your readers are likely to want to see but which are
either peripheral to the argument or too bulky to put in the body of the thesis.
Note: Most of the illustrative pages that follow have been taken directly from various theses submitted
in the past; not all pages come from the same thesis. Some changes have been made in these pages in
order to illustrate various conventions. All have been used with permission of the original author;
alterations in the original have also been permitted by the authors.
20
If your thesis involves mathematical symbols and formulae, you will find
great benefit in composing your manuscript using LaTeX or REVTeX,
macro sets of a computer language called TeX (rhymes with “blecch”).
LaTeX can be purchased on CD ROM or downloaded (21 MB) free of
charge from one of the sites of the Comprehensive TeX Archive Network
(CTAN) www.openresource.com/openres/archives/P/CTAN.shtml. For
more information, point your Internet browser to the Website of the TeX
Users Groups (TUG) at www.tug.org. The supplementary REVTeX macros
may be retrieved through the American Institute of Physics (AIP) Author
Services Compuscript Program at www.aip.org/pubserv/compuscript.html.
21
All information should be
centered horizontally
between the margins as
shown.
AIP / LaTex — SAMPLE TITLE AND SIGNATURE PAGE
The title must be in all
capital letters and located
2" from the top edge of
the page. If the title is
longer than five inches, it
must be split and placed
on two or more lines, with
the first line longest and
subsequent lines shorter
(inverted pyramid style).
THE USE OF GENETIC ALGORITHMS IN MULTILAYER
MIRROR OPTIMIZATION
Your name should be
double-spaced below the
word "by."
by
Shannon Lunt
Begin the statement with
the formal introduction
"Submitted to," and write
out the full name of
Brigham Young
University.
Submitted to Brigham Young University in partial fulfillment
of graduation requirements for University Honors
List your university
department, followed by
the date of submission,
month and year.
At the bottom of the title
page, provide signature
lines for your Thesis
Advisor and the chair of
your defense.
Department of Physics
March 1999
Advisor: R. Steven Turley
Honors Dean: Steven E. Benzley
Signature:
Signature:
AIP / LaTeX STYLE — ACKNOWLEDGMENTS PAGE
An acknowledgments
page is optional. If
included, it should follow
the signature page and
precede the table of
contents.
The heading should
match the heading style
of the abstract and table
of contents, in this
document 12 point bold
ulc (upper and lower
case), centered.
The acknowledgments
page is used to express
appreciation for
committee members,
mentors, family, or
friends who provided
assistance or support to
the writer during the
Thesis project.
Acknowledgments
should be brief, simple,
and in good taste.
(Please note that this
sample acknowledgment did not come from
the author of the thesis
modified for illustration
purposes here.)
Acknowledgments
I would like to give special thanks to Dr. Paul B. Savage for his instruction and
patience—and for having enough faith in me to allow me to work on this project.
I would also like to thank Chunhong Li for his continued example, patience, and for
teaching me to think like a scientist. Finally, I want to thank all of the researchers in
Dr. Savage's lab for their help, and for providing an atmosphere that made working fun.
ii
AIP / LaTex STYLE — SAMPLE CONTENTS PAGE
Contents
1. Introduction
5
1.1 Interest in the XUV Region . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.2 IMAGE Mission —XUV and Specifications . . . . . . . . . . . . . . . . . . . . . . . . 6
1.3 Optimization Techniques . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.3.1. Local Optimizers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.3.2. Global Optimizers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
1.4 Calculation of Reflectivities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
1.5 Reflectivity of X Rays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
1.6 A New Application of the GA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
2 Genetic Algorithm
2.1 Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.2 The GA Applied to the IMAGE Mission . . . . . . . . . . . . . . . . . . . . . . . . . .
2.3.1. Materials and Thickness . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.3.2 Study of Seeds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.3.3. Selecting Parents and Reproduction . . . . . . . . . . . . . . . . . . . . . . . . .
2.3.4 Merit Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.3.5 Hybrid Used . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
15
15
17
18
18
20
23
24
3 Results
3.1 Mirrors Designed for the IMAGE Mission . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.2 Periodic and Aperiodic Designs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.3 Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.4 Polarizers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.5 Selection of Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.5.1 Study of Population Size . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.5.2 Optimal Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
26
26
28
30
31
31
32
35
4 Conclusion
4.1 Where the GA is Valuable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.2 Rules for Application of the GA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.3 Future Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
36
36
36
37
Appendixes
A. Code for Genetic Algorithm Used in the Calculations . . . . . . . . . . . . . . . . . . . .
B. List of Materials and their Optical Constants . . . . . . . . . . . . . . . . . . . . . . . . .
38
38
67
iii
AIP / LaTex STYLE — LISTS OF FIGURES AND TABLES
List of Figures
1
2
3
4
5
6
Graph of a one-dimensional solution space . . . . . . . . . . . . . . . . . . . . . . . .
Diagram of Snell’s Law . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Multiple reflections from multilayers . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Geometry for the Parratt recursion formula . . . . . . . . . . . . . . . . . . . . . . . .
Composition of the chromosomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Flow chart of the Genetic Algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7
10
12
13
15
22
List of Tables
1
2
3
4
5
Terminology in the GA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Parameters specific to each application of the GA . . . . . . . . . . . . . . . . . . . . .
Study of 4-layer mirrors designed with different seeds . . . . . . . . . . . . . . . . . .
Study of 10-layer mirrors designed with different seeds . . . . . . . . . . . . . . . . .
Study of 16-layer mirrors designed with different seeds . . . . . . . . . . . . . . . . .
iv
17
18
19
20
24
AIP / LaTex STYLE — SAMPLE ABSTRACT PAGE
The abstract should be a
clear, concise summary of
the principal facts and
conclusions of the paper,
organized to reflect its
pattern and emphasis.
Complete and intelligible
in itself, its length should
be approximately 5% of
the length of the paper,
and no more than 500
words.
Type the paragraph in the
same font as the body of
the paper, double spaced,
preferably as one paragraph of continuous text.
Abstract
This paper describes the genetic algorithm applied to multilayer mirror optimization, including an explanation of how genetic algorithms work, as well as a description
of how this algorithm was applied to the design of bifunctional mirrors for the IMAGE
mission. This discussion is followed by the presentation of findings that contradict previous design rules for multilayer mirrors, including instances of aperiodic mirrors performing better than period mirrors, and an oxide producing a better design than a mirror
with solely elements as materials. Using the genetic algorithm, the best mirror design
found for the IMAGE Mission was an aperiodic Y2O3/Al 16 layer stack on SiO2. This
design had a predicted reflectivity of 36% at 304 Å and .2% at 586 Å.
v
AIP / LaTeX STYLE — SAMPLE HEADINGS AND CITATIONS
A variation in style used
in many scientific
publications, and
produced by the LaTex
macro, calls for a
numerical subordination
in headings, as illustrated.
Note that right margins
are justified, and that the
first paragraph under a
new heading is not
indented.
I. INTRODUCTION
1.1
Interest in the XUV Region
Much is known about the physics of the interaction of radiation with matter in the extreme
ultraviolet (XUV) or soft x-ray region. Some applications are developing that take advantage of what is currently known and extend the understanding of this region. To image an
object, light a wavelength less than the size of the object must be used. Since most cells
are on the order of a micrometer in size, soft x-rays, which are on the order of hundreds
of angstroms (Å), can be used to “see” these objects.
1.2
IMAGE Mission — XUV and Specifications
Another application in the XUV and the topic of this paper was to design a mirror for the
XUV section of the IMAGE Mission which will be launched in January 2000 and whose
goal is to image the magnetosphere. The mirror was specified at 14.5 degrees from normal to be highly reflective (>20%) at 304 Å to see the He-II lines from the magnetosphere
and to be non-reflective (<.2%) at 584 Å . . . . .
1.3 Optimization Techniques
When there is a problem with one or more independent variables, it is often desirable to
maximize or minimize a characteristic merit function, otherwise know as optimization.
1.3.1 Local Optimizers
Two types of local optimizers use different approaches: those that find the direction in
which the value of the function is decreasing by blind searching, and those that use information about the gradient of the solution space to find a minimum. One of the simplest
optimization techniques is the downhill simplex method developed by Nelder and Mead
and explained in Numerical Recipes [10]. The solution space in encoded into a simplex—a multidimensional shape. The second type of local optimization requires the comCitations are made by a
reference number, in
brackets, pointed to a
numbered list of sources
at the end of the document.
putation of derivatives. An example of this is the conjugate gradient method [10].
1.3.2.
Global Optimizers
A global optimizer is one which samples most of the solution space and is more apt to find
the global extreme rather than just a local extreme. Global optimization procedures such
Pages are numbered at
center bottom of each
page, beginning with the
first page of the body of
the text and continuing
through references and
Appendixes.
as simulated annealing [8, 9] and genetic algorithms [3] are able to handle these difficulties well and are less sensitive to an initial guess.
1
AIP / LaTeX STYLE – REFERENCES PAGE
References
The references appear in
a single numbered list at
the end of the paper,
arranged either
alphabetically by authors’
names or in order of first
appearance of each
source in the text, as
specified within the
guidelines governing the
research.
For references to
materials from the
Internet, give the full URL.
Capitalization styles vary.
This list uses headline
style for books and titles of
periodicals, and sentence
style for titles of periodical
articles.
Note that months of
publication are
abbreviated, without
periods.
[1] Ethan A. Merritt, The Kramers-Kronig Equation, 1996, Online posting, http://brie.bmsc.washington.edu/
Scatter/AS.kk.html ,30 Jan 1999.
[2] Eberhard Spiller, Soft X-Ray Optics, Bellington, WA, SPIE Optical Engineering Press, 1994.
[3] J. Michael Johnson and Yahya Rahmat-Samii, “Genetic algorithms in engineering electromagnetics,”
IEEE Antennas and Propagation Magazine, 39, Aug 1997, pp. 7-21.
[4] Masaki Yamamoto and Takeshi Namioka, “Layer-by-layer design method for soft-x-ray multilayers,”
Applied Optics, 31, Apr 1992, pp. 1622-1630.
[5] V.G. Kohn, “On the theory of reflectivity by an x-ray multilayer mirror,” Phys. Stat. Sol. (b), 187,
1995, pp. 61-70.
[6] L.G. Parratt, “Surface studies of solids by total reflection of x-rays,” Physical Review, 45, 1954,
pp. 359-369.
[7] Grant R. Fowles, Introduction to Modern Optics, New York, Dover Publications, 1975.
[8] T. Boudet, P. Chaton, L Herault, G. Gonon, L Jouanet, and P. Keller, “Thin-film designs by
simulated annealing,” Applied Optics, 35, 1996, pp. 6219-6226.
[9] Aleksandra B. Djurišig, Joven M. Elazar, and Aleksandar D. Rakig, “Simulated-annealing-based
genetic algorithm for modeling the optical constants of solids,” Applied Optics, 36, 1997, pp.
7097-7103.
This list uses et al. only
when a work has more
than six authors.
[10] William H. Press, et al., Numerical Recipes in C: The Art of Scientific Computing, New York,
Cambridge University Press, 1992.