Computational Sciences

Ph.D. Student Handbook

Middle Tennessee State University
http://www.mtsu.edu/COMS

Facebook – MTSU Computational Sciences Program

“The most scientifically important and economically promising research

frontiers in the 21st century will be conquered by those most skilled with
advanced computing technologies and computational science
applications.”

-Computational Science: Ensuring America’s Competitiveness, President’s

Information Technology Advisory Committee, 2005

Applied Mathematics
And Numerical Methods

Computational
Science

Computer Science
Science Discipline
 Computational Science Program Mission Statement

The mission of the Computational Science doctoral program is to prepare our students
for 21st research careers in academia, government, and industrial laboratories by
emphasizing the key role of computation in the physical, biological, and mathematical
sciences. Research-intensive studies in computing, mathematics, and science provide
the foundation needed to solve real world problems across the disciplines. Our
program emphasizes both simulation and data-intensive science, giving our students
the skills they need to model complex systems and handle the huge volumes of data
generated in modern scientific experiments. Our partnership among Biology,
Chemistry, Computer Science, Mathematical Sciences, and Physics and Astronomy
faculty results in a unique interdisciplinary education that prepares graduates to adapt
and grow as computing systems and scientific research evolves.

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Computational Science
DR. JOHN WALLIN, PROGRAM DIRECTOR
WISER-PATTEN SCIENCE HALL, 217
jwallin@mtsu.edu ~ 615-494-7735

The Computational Science Ph.D. is an interdisciplinary program in the College of Basic

and Applied Sciences and includes faculty from the departments of Biology, Chemistry,
Computer Science, Mathematical Sciences, and Physics and Astronomy. This program is
research intensive and applied in nature, seeking to produce graduates with
competency in the following three key areas:
1. mastery of the mathematical methods of computation as applied to scientific
research investigations coupled with a firm understanding of the underlying
fundamental science in at least one disciplinary specialization;
2. deep knowledge of programming and computing so that graduates can adapt
and grow as computing systems evolve; and
3. skills in effective written and oral communication so that graduates are
prepared to assume leadership positions in academia, national labs, and
industry.

The aim of the Computational Science Ph.D. is to be research intensive and applied.
From the beginning of their time on campus, students will be involved in research
groups and exposed to the breadth of interdisciplinary problems being addressed by
individual faculty members and their collaborations. A key goal of the coursework and
the early involvement in research is to help students achieve a broader view of
computational science as an approach that can be applied within and across traditional
disciplines. Graduates of the Ph.D. in Computational Science will be prepared with a
unique mix of skills that will permit them to pursue research careers in academia,
government, and industry laboratories. A strength of the Ph.D. in Computational Science
is the individual attention available to the students and the strong mentoring
relationship between the program faculty and the students.

Admission Requirements
Admission is based on a comprehensive assessment of a candidate’s qualifications
including Graduate Record Examination (GRE) scores, undergraduate and graduate
grade point average, and letters of recommendation.
Applicants who do not meet these minimums but whose application materials indicate
high potential for success may be admitted conditionally. Such students must meet the
conditions of their admission in the time stated to remain in the program of study.

Application Procedures
All application materials are to be submitted to the College of Graduate Studies

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The application deadline is February 15 for those wishing to be considered for graduate
assistantships for the following fall. Late applications may be considered, but admission
and financial support in the form of an assistantship is not guaranteed.

Applicants must:

1. submit an application with the appropriate application fee (online at

www.mtsu.edu/graduate/apply.shtml),

2. submit official scores for the verbal, quantitative, and analytical writing
measures of the GRE that indicate potential for success in the Computational
Science program. The GRE is an important measure and is given significant
consideration in the admissions review process. Successful applicants
typically have Verbal and Quantitative scores at or above the 50th percentile
for persons intending graduate study in science with a combined V + Q score
exceeding 1,000,

3. submit official transcripts showing a GPA in previous academic work that

indicates potential for success in advanced study. Successful applicants
typically have a minimum 3.5 GPA in their graduate work or a minimum 3.0
GPA when entering with a bachelor’s degree. Applicants should hold a
bachelor’s, master’s, or doctoral degree in a science discipline, and

4. provide letters of recommendation from at least three professors or

professionals that address the applicant’s potential to successfully complete
a Ph.D. in the Computational Science program.

Degree Requirements
The Ph.D. in Computational Science requires completion of 72 semester hours.
Additionally, candidates must:

1. make at least two research presentations at regional, national, or international

meetings as the lead or coauthor,

2. be lead author or make significant contribution as coauthor of two articles

published, in press, or under review in high quality, peer reviewed journals, and

3. in collaboration with an MTSU faculty member serving as principal investigator,

make a significant contribution to the development of at least one external grant
proposal.

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Curriculum
Foundation Courses (11 hours)
COMS 6100 (3 credits) Fundamentals of Computational Science
COMS 6500 (4 credits) Fundamentals of Scientific Computing
CSCI 6020 (4 credits) Data Abstraction and Programming Fundamentals

Computational Science Core (26 hours)

COMS 7950 (2 credits) Research Seminar in Computational Science
COMS 7100 (4 credits) Applied Computational Science
COMS 7300 (4 credits) Numerical Methods
COMS 7800 (3 credits) Teaching Internship
CSCI 7300 (3 credits) Scientific Visualization and Databases
CSCI 6050 (4 credits) Computer Systems Fundamentals
CSCI 6330 (3 credits) Parallel Processing Concepts
MATH 7450 (3 credits) Mathematical Modeling I

Electives (19 hours)

Three courses from the following, selected in consultation with the major professor and
dissertation committee.
BIOL 6350 (3 credits) Biostatistical Analysis
BIOL 6390 (3 credits) Advanced Cell and Molecular Biology
BIOL 6450 (3 credits) Advances in Molecular Genetics
BIOL 6760 (3 credits) Bioinformatics
CHEM 7720 (3 credits) Advanced Topics in Physical Chemistry
CHEM 7400 (3 credits) Computational Chemistry I
CHEM 7410 (3 credits) Computational Chemistry II
CSCI 6100 (3 credits) Analysis of Algorithms
CSCI 6130 (3 credits) Selected Topics in Parallel Processing
CSCI 7350 (3 credits) Data Mining
MATH 6260 (3 credits) Advanced Differential Equations I
MATH 6300 (3 credits) Optimization
MATH 7750 (3 credits) Mathematical Modeling II
STAT 7400 (3 credits) Computational Statistics
PHYS 7400 (3 credits) Computational Physics I
COMS 7100 (3 credits) Special Topics
COMS 7654 (3 credits) Professional Seminar

Directed Research (6 hours)

Students must complete 6 hours of Directed Research before advancement to candidacy
COMS 7500 (1-3 credits) Directed Research in Computational Science

Dissertation (12 hours)

COMS 7640 (1-6 credits) Dissertation Research

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Program Notes

Applicants holding a master’s degree will be expected to have earned at least 21 semester hours
of graduate mathematics, science, or engineering credit with evidence of strong mathematical
skills and experience in computer programming through coursework, employment, and/or
research experiences. Applicants applying from the baccalaureate level must have an
appropriate science degree with evidence of strong mathematical skills and experience in
computer programming through coursework, employment, and/or research experiences.

Students entering with a master’s degree in mathematics, a science, or an engineering discipline

may, on the recommendation of the program coordination committee and with the approval of
the graduate dean, have up to 12 credit hours accepted from their master’s if it directly
corresponds to coursework in the Computational Science curriculum.

Applicants lacking necessary foundational coursework in previous degrees will be required to

complete these courses as part of their program of study in addition to the degree
requirements.

Candidates must file a degree plan in the College of Graduate Studies prior to the completion of
30 credit hours.

Candidates must file a Notice of Intent to Graduate Form in the College of Graduate Studies
within the first two weeks of the term in which the student intends to graduate.

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Retention and Graduation Information

Students must meet the expectations of the university as regards adequate progress toward the
degree. Specifically:

1. Doctoral students are expected to maintain a 3.25 grade point average for all graduate
coursework.
2. Students may not enroll in more than one semester before full admission is granted.
3. Students must complete and submit a Degree Plan form by the time two semesters are
completed.
4. Students are expected to consistently enroll in and complete coursework in their area of
study, making continuous progress toward attainment of the degree.
5. Once admitted to candidacy and enrolling in dissertation (COMS 7640), students are
expected to maintain continuous enrollment.
6. At least two thirds of the credits counted toward the degree must be at the 7000 level.

Additional Graduation Requirements

Because the aim of the Computational Science Ph.D. is to produce students who are fully
prepared to pursue research careers in academia, industry, and at national labs, the
Computational Science Ph.D. program will put in place a series of benchmarks to be
accomplished as the student progresses along the path to graduation. The benchmarks fall into
three specific categories. Students must:

1. Make at least two research presentations at regional, national or international meetings

as the lead or co-author.
2. Be lead author or make significant contribution as co-author of two articles published, in
press, or under review in high-quality peer-reviewed journals.
3. In collaboration with an MTSU faculty member serving as principal investigator, make a
significant contribution to the development of at least one external grant proposal.

Although some of these expectations would be realized naturally in the course of a student‘s
progress towards the Ph.D., the Computational Science program at MTSU makes them explicit to
emphasize to incoming students the expectation that they will become active and engaged
participants in the research process. Publications and presentations are already recognized as
standard metrics of research progress. The involvement of Ph.D. students in the grant writing
process is a developing trend designed to train graduates to be more effectively prepared for
jobs in the research environment. Experience in grant writing is both a necessary skill and an
important insight into the manner in which science and engineering are funded. Because grant
agencies require the principal investigator (PI) to have a permanent academic position, the
grant will be written in collaboration with the major professor who will serve as the PI.

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Milestones and Expectations for students in the Computational
Sciences PhD Program at Middle Tennessee State University

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When What
During your first year Students will find a pre-dissertation advisor
and a form a pre-dissertation committee
within the first year of their studies. This
committee will be used to establish a
preliminary program of study and oversee
the preliminary exam.
The summer after your first year Students will complete a qualifying exam.
The qualifier will be created by the student’s
advisor, the student’s committee, and in
consultation with the program director. The
exam will be in the form of a take-home
computational research project that takes
between 2 and 4 weeks. At the end of the
project, the student will prepare a short (30
minute) talk and present it to the committee.
The committee will ask questions about the
work and other subjects. The committee will
vote on whether the student’s performance
was satisfactory. The student will be given
the opportunity to repeat this process if the
results were unsatisfactory.
Upon Completion of the Qualifier Students will choose their dissertation
advisor and the members of their
dissertation committee before their course
work has been completed. These may be the
same as in the pre-dissertation committee.
When most of the student’s coursework is Student will create a prospectus for their
done research work. This will include a literature
review, research plan, milestones, and other
appropriate information needed for the
committee to judge the impact and likelihood
of success of the research. The student will
provide a written copy of this prospectus to
the committee and present to the committee
orally. The committee may make
recommendations to the student about the
direction of their dissertation, and decide if
the student is qualified to advance to
candidacy for a PhD at this meeting. After
satisfactory completion of the prospectus and
the oral presentation, the student will have
completed his preliminary examination. It is
anticipated that the student will reach this
milestone one or two years before their final
defense.

During their dissertation research or Students will help write a proposal to a major
before funding agency in collaboration with their
advisor
During their dissertation research or Students will be the lead author or a make a
before significant contribution as co-author to at
least two papers to articles published, in-
press, or under review in a peer-reviewed
journal.
During their dissertation research or Make at least two research presentations at
before regional, national, or international meetings
as the lead or co-author 9
At least one month before the final Students will present a final draft of their
defense dissertation to their committee and schedule
Qualifying Exam Guidelines

The student will form a pre-dissertation committee to supervise their Qualifying

Exam. This committee will be composed of three faculty members associated with
the COMS program. The committee members must come from at least two
departments. This committee will help advise the student until the final dissertation
committee has been formed.

After discussions between student and the pre-dissertation committee, a topic and
timeline for the Qualifying Exam will be submitted to the COMS Program Director for
final review. This form will be submitted to the Director for review at least four
weeks before the project presentation date. It is expected that students will
complete the qualifying exam during their first summer in the COMS program as part
of their on-going research.

The exam itself will be in the form of a take-home Computational Science research
project that takes between 2 and 4 weeks to complete. This topic may be associated
with on-going research with the student’s advisor, but should test the ability of the
student to conduct an independent research project in Computational Science. At
the end of the project, the student will present a short (30 minute) talk to the pre-
dissertation committee along with a short paper summarizing the results. The
committee will ask questions about the qualifying exam project and other subjects as
appropriate. At the end of the presentation, the committee will decide if the
student’s performance was satisfactory. If the committee feels the student’s
performance is unsatisfactory, the student will be given one additional chance to
complete this exam.

The qualifying exam should:

 Include programming beyond Matlab and should include at least basic data
structures
 Involve the use of numerical methods
 Have a direct connection to a scientific domain – not just computer science or
mathematics
 Connect to the scientific literature
 Involve a simulation or data intensive project

Forms for the qualifying exam are available from the Program Director.

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Dissertation Proposal Guidelines

The purpose of the dissertation proposal is to delineate the expectations and

requirements for the Ph.D. dissertation. The proposal should place the student’s
current and future work into a broader context, show the likely outcomes and goals of
the current work, and describe the significance and risks of pursuing this line of
research. Overall, this is a proposal that needs to be reviewed and negotiated with the
dissertation advisor and the dissertation committee.

A dissertation proposal is typically about 20 pages long including figures and

references. Some proposals are shorter and some are longer. There isn’t an exact
format. However, there are some elements that are common to good dissertation
proposals. They can be combined into different sections, but the elements include:

1) Introduction – The introduction includes a thorough literature review of the subject

of the dissertation. It has to provide enough material and background information that
outside members of the committee can understand the research questions and issues
associated with the student’s research area. It should include information about both
the answered and unanswered question in the field. It should also show the reader
that this is an active research field.

2) Proposal Objectives – After explaining what has been done, the student needs to put
his/her work and its significance into the context of the review. This process is
partially done by showing the unanswered questions in the field and why they are
important. However, it also should include some justification about why the student
has the ability and tools needed answer these questions. Some discussion should be
included about how significant these results will be as evidenced by the literature. The
idea at this point is to outline the broader view of what will be done leaving some of the
specifics for later in the proposal.

3) Methodology – After defining the problem, the reader needs to understand how the
student will be approaching his/her work. A description of the equations, algorithms,
codes, and relevant data needs to be created to allow faculty to understand the methods
involved. The relevant numerical methods can be particularly important in
understanding the work.

4) Verification and Validation plan – Although defining the methods used is critical, the
reader also needs to be able to trust the results of the dissertation. The student should
create a plan to verify the code and validate the result. Typically this includes a
combination of reproducing well understood problems with analytic solutions,
comparisons to existing results in the field, and some types of internal consistency
checks. These checks need to be spelled out.

5) Expected timeline and milestones – The committee and the student need to have an
expected timeline for the work being proposed. The timeline should include notable
milestones in the work including submission of manuscripts to journals, conference
papers, and proposals being submitted. It should also include time for software

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development, analysis, and write-up. Work already completed should be included in
this timeline to show that progress has already been made in the research.

6) Resources, risks, and contingencies – Some mention of the risks in the research plan
and the plans to address these risks needs to be made. The student needs to show that
this work is possible to complete. The student and the committee also need to have
some plan if the research is unsuccessful – for example if the methodology being used
doesn’t produce satisfactory results or if the development time for software ends up
being much longer than expected. Having a good understanding of the research
priorities and the likelihood of them being successful is very important in dissertation
planning. It is also important to address the resources needed for the work. In
Computational Science, this is typically the computer time and date storage
requirements for completing the work.

7) Publications and significance – The committee needs to understand the expected

publications that will result from the research. Ideally this would include specific titles,
journals, and conferences for the work that are aligned with the project milestones.
The student also needs to put the results in a broader context to show the significance
of their research in the field. Primarily this means demonstrating that their work will
be useful to other scientists.

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Graduate Teaching Assistants
Students in the COMS program who have a graduate teaching assistantship (GTA) will be
assigned a department for their teaching assignments. A full time GTA is expected to work 20
hours per week on their teaching assignment. Most teaching assistants will perform one or
more of the following responsibilities:

 Teaching a classroom section of a course

 Teaching a laboratory or discussion section of a course
 Tutoring or providing special assistant to students of the University
 Assisting a faculty member in grading, advising, or other duties necessary to conduct a
course
 Assisting directly or indirectly in instruction or supervision of MTSU students in
community programs, internships, workshops, or seminars for practicing professionals

Full-time Graduate Assistants will work:

• Six (6) contact hours per week in classroom or laboratory instruction in which the GTA
assigns the grade;
• Eight (8) contact hours per week in laboratory supervision in which the professor assigns the
grade;
• Twenty (20) clock hours per week in supervised activities in the department or office of their
employment; or
• A combination of above, not to exceed these workloads.

The particular teaching assignments will depend on the department assigned by the Program
Director and the individual department’s teaching needs. The department will report back to
the program if you are performing in a satisfactory manner as a GTA. Students also must
maintain a 3.25 GPA to keep your assistantship and enroll in at least 6 credits during the Fall
and Spring semesters.

All Graduate Assistants are to meet the workload requirements as set forth in the MTSU
Standard Assistantship Contract. Failure to fulfill the terms of this contract can result in a
termination of the student's assistantship at any time without advanced notice.

Graduate Research Assistantships

Duties vary according to the nature of the department and/or the specific research project to
which the student is assigned. The student may assist a faculty member in his/her research or
may be part of a team working on an externally funded research project. The duties of a
Research Assistant are performed under the direction and supervision of members of the
faculty or academic staff.

Summer Research Activities

During the summer, students on GTA will continue to get paid However, the student’s duties
will primarily be to work on research projects associated with your degree while working
under the direction of your research advisor. A full time GRA is expected to work at LEAST 20
hours per week on research projects during summer and meet with their research advisor on a

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regular basis. During the summer, students must register for at least 3 credits of course work.
Often, this is just a directed research course.

Ultimately, the Ph.D. is a research degree. Before students can graduate, they will need to
publish two papers in refereed scientific journals. The only way this can happen is by devoting
a large amount of time on research work that goes well beyond the minimum requirements for
the assistantship. Most students will take a combination of seminar and/or directed research.
Graduate students at other institutions typically work MORE than 40 hours per week doing
their research. Since you will eventually be competing with these other students for jobs, it is
definitely in your interest to spend much more than the minimum amount of required time on
your research activities during the summer.

As a GTA or GRA, students are expected to be on campus at LEAST 20 hours per week –
including during summer. Students need to be here to interact with your advisor and with
other students. This is a job, and you have to come to work.

Summer Internships
First and second year students are encouraged to apply for summer internships offer through
National Laboratories, including Los Alamos, Oak Ridge, Naval Research Laboratory, and Arnold
Engineering Center. Summer programs and workshops at National Laboratories typically last
about 10 weeks and often offer competitive stipends. Admission into these programs is usually
very competitive. These programs can help students develop professional connections and real
world experience in Computational Science. Unfortunately, many of these summer programs
are only available to American Citizens. More advanced students are advised to carefully
consider how such an internship will affect their dissertation research. Students chosen for a
summer fellowship should notify the program Director as soon as possible. Since students
can’t be paid from two different sources, we generally need to terminate the summer portion of
the GTA for participating students. The GTA would start up as normal in August when the
student has returned back to campus.

Graduate Fellowships
The Department of Energy and the National Science Foundation both offer graduate fellowship
opportunities for highly qualified students. These are highly competitive, but we encourage
highly qualified students to apply to these programs.

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Computational Science Faculty Members

Biology (BIOL)
 R. Stephen HowardProfessor(615) 898-2044rshoward@mtsu.edu

Chemistry (CHEM)
 Tibor KoritsanszkyProfessor(615) 904-8592tkoritsa@mtsu.edu
 Preston MacDougallProfessor(615) 898-5265pmacdoug@mtsu.edu
 Anatoliy VolkovAssoc. Professor(615) 494-8655avolkov@mtsu.edu

Computer Science (CSCI)

 Hyrum CarrollAsst. Professor(615) 898-2801hcarroll@mtsu.edu
 Cen LiProfessor(615) 904-8168cli@mtsu.edu
 Chrisila Pettey Professor(615) 898-2397cscbp@mtsu.edu
 Suk Jai Seo Professor(615) 904-8292sseo@mtsu.edu
 Roland Untch Professor (615) 898-5047 untch@mtsu.edu

Geosciences (GEO)

 Henrique MommAsst. Professor(615) 904-8372henrique.momm@mtsu.edu

Mathematical Sciences (MATH)

 Wandi DingAsst. Professor(615) 494-8936wding@mtsu.edu

 Don HongProfessor(615) 904-8339dhong@mtsu.edu
 Abdul KhaliqProfessor(615) 494-8889akhaliq@mtsu.edu
 Yuri MelnikovProfessor(615) 898-2844ymelniko@mtsu.edu
 Zachariah SinkalaProfessor(615) 898-2679zsinkala@mtsu.edu
 D. Chris StephensAssoc. Professor(615) 494-8957cstephen@mtsu.edu
 Qiang Wu Asst. Professor(615) 898-2053 qiang.wu@mtsu.edu
 Dong Ye Asst. Professor(615) 898-2669 dong.ye@mtsu.edu
 Xiaoya ZhaProfessor(615) 898-2494xzha@mtsu.edu
Physics and Astronomy (PHYS)
 William RobertsonProfessor(615) 898-5837wroberts@mtsu.edu
 John WallinProfessor & Director(615) 494-7735jwallin@mtsu.edu

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People and On-Line Contact Information

Program Website
http://www.mtsu.edu/COMS

Facebook – MTSU Computational Sciences Program

Socials – TBA

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