BIOPHYSICS Handbook 2011 8-26-11 by xuyuzhu

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									Biophysics                              University of Michigan




         GRADUATE STUDENT
             HANDBOOK




              Updated August 26, 2011
INTRODUCTION

This Handbook serves as a guide to the rules and regulations of the Biophysics Graduate Program as well as that
of the Rackham Graduate School here at the University of Michigan. As a student you should familiarize yourself
with requirements of the Biophysics program and the requirements of the Rackham Graduate School. Throughout
the Handbook references are made to Graduate School rules which can be found in their entirety in the Rackham
Graduate Student Handbook. For counseling, consult with the Graduate Chair or the Student Services
Administrator. Students in research groups should always consult their thesis mentor first.
Biophysics at Michigan is inter-disciplinary and multi-disciplinary research, distinct from the Ph.D. Programs in
Physics, Chemistry, Biological Chemistry, or Biology. It encompasses fields as different as structural biology (X-
ray and NMR structure determinations), biomolecular spectroscopy (NMR, IR, UV, EPR), computational
biophysics (protein structure prediction, ab initio forcefield calculations), cellular biophysics (biomolecular
mechanics, manipulation of single protein molecules, receptor diffusion in membranes) and biophysical chemistry
(peptide design, protein folding, thermodynamics). The degree in Biophysics is conferred in recognition of
independent, insightful and physically-oriented investigations of biological processes, matter or theories as
demonstrated in a thesis based upon original research and creative scholarship. It is the mission of the Biophysics
graduate program to help students prepare for a career in Biophysics by coordinating their course work, research
endeavors, teaching commitments and financial aid.
There is no independent Master of Science (M.S.) program in the Biophysics Graduate Program and the Program
will not admit students intending to obtain a terminal Master of Science Degree.
Related information can be found on the Biophysics website www.biop.lsa.umich.edu. This handbook
supersedes the website.
                                                               TABLE OF CONTENTS


WHERE TO GO FOR INFORMATION ........................................................................ 3
DEPARTMENT STAFF.................................................................................................... 4
CONTINUOUS ENROLLMENT POLICY .................................................................... 5
GRADUATE SCHOOL REQUIREMENTS................................................................... 5
BIOPHYSICS GRADUATE PROGRAM REQUIREMENTS ..................................... 6
  COURSES .............................................................................................................................................................................. 6
  STARTING RESEARCH ....................................................................................................................................................... 6
  GRADUATE STUDENT INSTRUCTORSHIP (TEACHING) ............................................................................................. 7
  PRELIMINARY EXAMS ...................................................................................................................................................... 7
  SEMINAR .............................................................................................................................................................................. 9
  THESIS RESEARCH ........................................................................................................................................................... 10
  THESIS COMMITTEE ........................................................................................................................................................ 10
  GOOD STANDING ............................................................................................................................................................. 10
  THESIS PREPARATION AND DEFENSE ......................................................................................................................... 11
  VACATION POLICY .......................................................................................................................................................... 11
  STUDENT REPRESENTATION ........................................................................................................................................ 12
  MASTERS DEGREE ........................................................................................................................................................... 12

FINANCIAL INFORMATION ...................................................................................... 12
FACULTY AND ASSOCIATED FACULTY MEMBERS ......................................... 14
TYPICAL CHRONOLOGY OF PH.D. DEGREE ....................................................... 15
COURSE REQUIREMENTS ......................................................................................... 15
SAMPLE CURRICULUM .............................................................................................. 16
COURSE DESCRIPTIONS ............................................................................................ 17
  A.      BIOLOGICAL CHEMISTRY .................................................................................................................................... 17
  B.      BIOMEDICAL ENGINEERING ................................................................................................................................ 18
  C.      BIOPHYSICS ............................................................................................................................................................. 18
  D.      CHEMISTRY ............................................................................................................................................................. 19
  E.      MATHEMATICS ....................................................................................................................................................... 20
  F.      MOLECULAR, CELL, & DEVELOPMENTAL BIOLOGY ..................................................................................... 20
  G.      PHARMACEUTICAL CHEMISTRY ........................................................................................................................ 21
  H.      PHYSICS .................................................................................................................................................................... 21
  I.      STATISTICS .............................................................................................................................................................. 22




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WHERE TO GO FOR INFORMATION

      Graduate Student Handbook
      This handbook is to be used as a guide to the rules and regulations that govern the graduate program
      both here in the Biophysics program as well as the University of Michigan. As a student you must
      familiarize yourself with requirements of the Department and the Rackham graduate school.
      Throughout the Handbook references are made to Rackham rules and regulations which can be found
      in their entirety in The University of Michigan Bulletin, Rackham Graduate Student Handbook on
      their website: http://www.rackham.umich.edu/.


      Email
      Each student will have a UM email address and account. Messages and information are sent to the
      graduate student group biophysics-gradstudents@umich.edu and on an as needed basis to individual
      students. Please check your email every day.


      Copy Room
      The copy room (#4029) is located on the 4th floor directly across from the Biophysics administrative
      office (#4028). If you need to make copies that are course or lab related, stop in the Administrative
      Office and you will be given a code for the copy machine. Once you join a lab, you will be given a
      lab-specific copy code to use.


      Graduate Mailboxes
      Every graduate student has their own mailbox located in the Biophysics lounge on the 4th floor (room
      4041). Any mail addressed to you here in Biophysics will be put there, as well as any messages from
      faculty, Academic Services staff, Technical staff or Rackham will be put in your mailbox. Please
      check your mailbox regularly.


      Biophysics Student Library
      Our library contains various Biophysics and related texts for student use. Please see someone in the
      Administrative Office for a key. The usual loan period is for 1 week. If you need more time, please
      contact Sara in the Biophysics main office.


      Bulletin Board
      The board is located outside of the Administrative Office (4028). You will find such information as
      Fellowships, Scholarships, Grants offered, Job listings, and other University business pertaining to
      graduate students.


      Graduate Academic Advisor
      First year students will see Professor Ayyalusamy Ramamoorthy for academic counseling. After
      your first year, your Research Advisor/PI will be your academic counselor.




                                                  3
DEPARTMENT STAFF


                Administration
                                                                               Room    Telephone*
                  Chair                               Jens-Christian Meiners   4028C   4-1146
                  Associate Chair,                    Hashim Al-Hashimi        4022    5-3361
                  Graduate Program
                  Administrative Manager              Jane Ginopolis           4040    5-7056
                  Executive Secretary                 Ann Titus                4028b   4-1146
                  Financial Analyst                   Kim Angelopoulos         4028    4-5258
                  Student Services Manager            Sara Grosky              4028    3-6722
                  Systems Administrator               Tony Markel              4019    7-2146
                  Research Engineer                   Keith Shaw               3012    3-2501


* When dialing from a campus phone, only the last five digits are used




                                                       4
CONTINUOUS ENROLLMENT POLICY
The Dean and the Executive Board of the Rackham Graduate School have approved the adoption of a continuous
enrollment requirement for Ph.D. students at the University of Michigan, to become effective in the Fall Term
2010.

Once admitted to a Ph.D. program, students will register every fall and winter term until their degree is awarded,
unless they are taking an official leave of absence. Please consult your Rackham handbook or Rackham’s website
for more information: http://www.rackham.umich.edu/policies/continuous_enrollment/.




RACKHAM GRADUATE SCHOOL REQUIREMENTS
The basic requirements for the degree of Doctor of Philosophy set by the Rackham Graduate School include:

    1.   Adherence to the Continuous Enrollment Policy
    2.   Completion of at least 18 hours graded graduate coursework on the Ann Arbor campus
    3.   Satisfactory academic standing (“Good Standing”)
    4.   Attainment of Candidacy (passing of Preliminary Exams)
    5.   Appointment of a Thesis Committee to supervise the student’s program and progress in research
    6.   Approval of the written dissertation by the Thesis Committee and Rackham, and a final examination by
         the Thesis Committee
    7. Minimum of four cognate credit hours – courses taken outside the Home Program. Undergraduate
         transcripts/credentials need to have been submitted to Rackham within seven years from the start of the
         current program.



BIOPHYSICS CREDIT REQUIREMENTS
The minimum requirement for the Ph.D. degree is seven (eight including the Final Term – six with a relevant
Masters) full time terms of study and research beyond the bachelor’s degree. A student is considered full time
with registration of 9 hours per term (8 hours after Candidacy). A graduate student research or teaching
assistant must be a full-time student. GSRA’s or GSI’s can be full time with 6 hours.
A minimum of 18 credits must be accumulated prior to admission to Candidacy. These hours include all regular
required program courses, any courses in which the student registers and pays fees as a visitor but exclude
Biophysics 890 (Rotation Research) and 990 (Pre-Candidate Research). A minimum of 6 credits each for 890 and
990 must also be completed in order to achieve candidacy. The number of hours registered for Biophysics 990
may range from one to eight per term as approved by the thesis mentor. A student must register for a total of 9
hours per term prior to Candidacy.
Following admission to Candidacy, the student must complete a minimum of 48 credit hours of 995. This balance
between the pre-Candidate and Ph.D. candidate-hours is made up by eight hours per term of registration in
Biophysics 995. A student must register for a total of 8 hours as a candidate. Students are allowed one extra
course on top of the 995 research credits, per Rackham guidelines.



Students should register for Fall & Winter terms only.


                                                         5
BIOPHYSICS GRADUATE PROGRAM REQUIREMENTS
Please note that Biophysics requirements include and supersede the Rackham requirements.
COURSES

It is the goal of the Program to make sure the student acquires a solid background in biology, biochemistry,
chemistry, physics, and biophysics, by including a selection of courses on the graduate or senior undergraduate
level. Establishing a solid academic foundation is especially important in a rapidly changing interdisciplinary
field such as Biophysics. In total, six courses are required. All students are expected to complete the four core
biophysics courses (BIOPHYS 520, 521, 550 and 595). Because of the interdisciplinary nature of Biophysics,
students enter the program from a variety of undergraduate backgrounds. Most students, unless they have an
unusually strong background in biology, will be expected to complete one course in cell biology and one course in
biochemistry. Students that lack a strong foundation in the physical sciences should take appropriate advanced
undergraduate courses or introductory graduate courses in quantum mechanics or quantum chemistry and in
thermodynamics or statistical physics. Pre-candidates must be registered for a minimum of 9 credit hours.
The course requirements begin on page 14, and their descriptions start on page 16. Each course is 2-4 credits
except as noted. Courses are counted towards the Biophysics Requirements only when they are passed; for
undergraduate courses (400-level) passing grade is “C” or above, in graduate courses (500-level and above),
passing grade is “B” or above. However, be aware that failed courses keep counting towards your cumulative
grade-point-average (GPA), which has to remain “B” or above at all times. (See “Good Standing” below.)
Students who are Doctoral Candidates (i.e. who have passed their preliminary exams) can take one additional
course for credit. Follow the rules given in the Rackham Handbook. Other classes may be audited (contact the
instructors). Visit is the Graduate version of audit (VI). Taking extra courses before and after Candidacy must be
discussed with the Thesis Mentor or with the Graduate Chair when the student has not chosen a home lab.
Grades in research courses accepted by the Graduate School are “S” (satisfactory) and “U” (unsatisfactory). No
credit is given for a “U” but RFT’s are earned if applicable. An “I” grade may be given in any lecture or
laboratory course when a minor part of the course work remains undone at the end of the term. If the work is
made up within two complete semesters, a supplementary report of the appropriate letter grade may be filed; after
the second semester the supplementary report will not be accepted and the “I” remains permanently on your
record. Check in the Rackham Handbook for specific information on the Incomplete Policy. An “I” always
remains on the record.

STARTING RESEARCH

The Ph.D. signifies the completion of a significant body of original publishable research, performed under the
supervision of a research advisor. The choice of a research advisor and thesis project is a major decision. This
choice is facilitated by a rotation program, which allows students to explore various research laboratories and
areas of Biophysics research during their first year. You should register for at least one term of Biophysics 890,
Introduction to Research, consisting of a laboratory rotation in the laboratory of any Program faculty member
upon mutual agreement. It is recommended that you carry out at least two semesters of Biophysics 890 rotations.
Even students sure of their choice of thesis advisor are encouraged to take advantage of this opportunity to
broaden their exposure to different research efforts.
Students are encouraged to choose their thesis lab before the start of their second year. You may join in the
laboratory of any of the regular or associated faculty. Since the thesis mentor will be responsible for the majority
of stipend, tuition and fringe benefits expenditures, it behooves the student to consider the financial position as
well as the scientific interest when choosing a lab. You should register for Biophysics 990 (Pre-Candidate
Research) during each semester of dissertation work as long as you are a pre-Candidate.
You must present an oral prospectus of your research project to your thesis committee after achieving candidacy.
This is not an exam, but a review to ensure that the project is indeed in the field of Biophysics, broadly defined,
and of an appropriate scope. After that, you should discuss your progress annually with your thesis committee.

                                                         6
You may decide at some point that you want to switch thesis labs; this is permissible. The decision is
consequential because the choice of a lab amounts to the choice of a research field that will affect much of your
future career. You are encouraged to switch only after serious reconsideration.
The student and the thesis mentor are jointly responsible for following the Program and Graduate School
requirements for the Ph.D. The mentor’s responsibilities begin at the time of his/her agreement to accept the
student for research. In addition to supervising the research, the thesis mentor is expected to advise the student on
course elections, examinations, independent study pertinent to his/her general development as a scientist and any
other matters affecting his/her general progress toward a degree.

GRADUATE STUDENT INSTRUCTORSHIP (TEACHING)

Although there are no formal teaching requirements, as part of their training students are strongly encouraged to
teach at least one semester as a Graduate Student Instructor (GSI) in Biophysics, Chemistry, Biology,
Biochemistry, or Physics. This experience is especially important for those interested in a future career in
academia, although all students can gain from the opportunity for presenting technical material in a pedagogical
context. It may happen that you are asked to teach in later stages of your study as well, depending on financial
resources of your thesis mentor (see “Financial Support”). Students are strongly encouraged to serve as teaching
assistants in a form that includes direct contact hours with a class (rather than grading). It is mandatory for
students assigned teaching positions for the first time to take a one-credit GSI Training Course associated with the
program in which you are teaching. This course is usually offered the last week in August.

PRELIMINARY EXAMS

Students are required to pass a three-part preliminary exam in order to attain candidacy. The three parts of the
exam cover Biochemistry and Cell Biology, Physics and Physical Chemistry, and Biophysics. The
Biochemistry/Cell Biology part will be at the level of Stryer’s Biochemistry. The Physics/Physical Chemistry part
will cover Quantum Mechanics/Quantum Chemistry and Thermodynamics/Statistical Mechanics at the advanced
undergraduate level, combined with Classical Mechanics and Electricity and Magnetism at a General Physics
(with calculus) level. The Biophysics part will be an original research proposal, presented to a panel of three
faculty members, addressing a question of current relevance in biophysics. These three parts can be taken and
passed independently of each other.

The Biochemistry/Cell Biology and the Physics/Physical Chemistry parts will be given in the winter term. It is
recommended that students with the appropriate undergraduate background take these parts during their first
semester, so as to establish competency in these particular areas. The Biophysics (oral) part will be given in May.
It is expected that students will pass this part at the end of their second year.

Students can take the exam parts as often as they are given. Students are expected to pass the preliminary exam
and required coursework and achieve candidacy by the start of their third year.

A preliminary list of topics to be covered by the exams is included below:

Biochemistry and Cell Biology Preliminary Exam Topics
At the level of Stryer’s Biochemistry
         Proteins
                o Amino acids
                o Peptide bond
                o Levels of protein structure
                o Sequencing of proteins
                o Characterization of proteins
                o Globular proteins – hemoglobin
                o Fibrous proteins – Collagen, silk, wool
                o Protein folding
                o Enzymes
                o Enzyme kinetics

                                                            7
                         Michaelis-Menten
                         Types of inhibition
                         Mechanisms
                         Regulation
      Lipids
            o Triglycerides
            o Phospholipids
            o Steroids
            o Membranes
      Carbohydrates
            o Glycolysis
            o Gluconeogenesis
            o Glycogen
            o Citric Acid cycle
            o Pentose phosphate pathway
            o Oxidative phosphorylation
      Nucleic Acids
            o Bases
            o DNA structure and replication
            o RNA structures, transcription, splicing
            o Protein synthesis
      Cell Biology
            o Cell architecture
      Nuclear structure
      Membrane structure
            o Cell trafficking
            o Signal transduction
            o Transport
            o Cell replication
            o Cell motility

Physics and Physical Chemistry Preliminary Exam Topics
      Classical Mechanics (at the level of General Physics (with calculus): Halliday and Resnick)
            o Forces, torques, momentum and energy of linear and rotational motion
            o Levels of protein structure
            o Gravitational attraction and potentials
            o Oscillatory motion including damped and forced harmonic oscillators
            o Coupled harmonic oscillators
            o Central force motion
            o Kinematics of two-particle collisions
            o Non-inertial reference frames; Coriolis force
      Electricity and Magnetism (at the level of General Physics (with calculus): Halliday and Resnick)
            o Electrostatics with dielectrics and multipoles
            o Maxwell’s equations in integral form
            o Electromagnetic waves
            o Polarization
            o Reflection and refraction
            o AC and DC circuits
      Quantum Mechanics (at the level of upper-class undergraduate physics or physical chemistry)
            o Uncertainty principle
            o DeBroglie wavelength
            o Schroedinger equation, expectation values, probability densities
            o Bound states in a square well, atom, and harmonic oscillator
            o Tunneling
            o First-order time-independent and time-dependent perturbation theory
            o Valence Bond theory and molecular orbitals
            o Delocalized orbitals
      Statistical Mechanics and Thermodynamics (at the level of upper-class undergraduate physics or physical chemistry)
            o First and second laws of thermodynamics and simple applications
            o Free energies, definitions and uses
            o Statistical definition of entropy
            o Ensembles
            o Partition functions
            o Kinetic theory of gases in equilibrium

                                                                8
            o   Phase transitions
            o   Boltzmann distribution

Biophysics Preliminary Exam Guidelines
The goal of the Biophysics Prelim Exam is to evaluate a student’s preparation for and ability to successfully
complete a Ph.D. thesis. Successful completion of a Ph.D. requires the ability to synthesize information from a
variety of sources. The Prelim exam is intended to evaluate a student’s ability to bring together the knowledge
learned in formal coursework and from readings of the research literature and to combine this information to
produce an original research proposal. This proposal (no longer than 10 pages single spaced, excluding figures
and references) will be evaluated by a candidacy committee. The committee will then meet with the student in an
oral exam at which the student will defend the proposal.

Selection of topic. Students are encouraged to make the proposal relevant to their interests, ideally a project that
could broaden and extend the work of their lab. The candidate should submit a one-paragraph summary of their
proposed Original Research Proposal to the Graduate Chair no later than the middle of their 4th semester in
residence (see the timeline below). Once this is approved, the candidate may begin preparation of the full
proposal.

Scope of proposal. The Original Research Proposal should utilize a variety of biophysical methods to address a
question of current scientific interest. Methodology should be described at the level of that discussed in
Biophysics 520 and 521. The proposal should include a review of the relevant background literature, although
this need not be an exhaustive review. The maximum length for the proposal is 10 pages, single-spaced, exclusive
of figures and references. References should be in the NIH style (include titles) and may not exceed 3 pages.
Candidates should note that longer proposals are seldom better proposals; the maximum length should not be
taken to represent the ideal length.

Preliminary (Candidacy) exam committee. A committee of at least 3 Biophysics faculty members and one
cognate (non-Biophysics) faculty member will review the proposal. This committee should not include the
candidate’s thesis advisor. With the addition of the thesis advisor, the prelim exam committee will often be
identical to the candidate’s Ph.D. committee (although this is not required). The Preliminary Exam Committee
must be approved by the Graduate Chair.

Timeline. The timeline assumes that students start in the fall and that they complete candidacy requirements
during their 4th semester (the winter semester of their second year). This timing takes advantage of the 1-month
grace period offered by Rackham for the Prelim (prelim month of May). Students that have a different schedule
should consult the graduate chair regarding timing.

 1. Selection of topic for proposal – by the end of March
 2. Completion of proposal – by the last day of finals for the winter semester.
 3. Defense of proposal to faculty committee – before the end of May after their 4th semester.
 4.   The 1 month grace period (May) for Prelims is for students who are registered full time the previous Fall
      and Winter terms.
SEMINAR

Students are required to present two seminars to faculty and fellow students. This offers you practice in
presenting a scientific lecture. One seminar is given as a seminar in the regular Biophysics Seminar Series and
takes place somewhere in the middle of your graduate career. It is recommended that you present your own
research. Should you decide to select a topic that is not your own research, consult with the Graduate Chair for
approval and/or assistance. The other seminar is a requirement for your thesis defense. You may be invited to
give yet another seminar in the regular Biophysics Seminar Series or other departments in the later stages of your
career. Students are encouraged to accept these invitations as they help develop good communication skills.



                                                          9
In addition to presenting a seminar, all students are required to attend the Biophysics Seminar Series. The serious
student will take advantage of all learning opportunities, and the Seminar Series represents excellent sources of
up-to-date results and ideas.

THESIS RESEARCH

When the formal course requirements and preliminary exams are completed successfully, then you will have
reached Candidacy status. Once you have obtained Candidacy, your main activity in Biophysics will be thesis
research. Every semester you should register for Biophysics 995 for 8 credit hours. You will also want to attend
many of the numerous specialized lectures and seminars at Michigan, and you may also want to take or audit
additional courses of interest to you. Normally, Candidacy should be achieved before the beginning of the third
year.
The thesis research should involve original and significant advances of our understanding of an important area in
Biophysics. It is expected that your work will result in papers published in peer-reviewed scientific journals. In
fact, the experiencing of presenting your work in written and oral form is an important part of the graduate
experience.

THESIS COMMITTEE

As the outlines of the research and preliminary results become clear, it is necessary to form a Thesis Committee
and present an introduction and progress report to them. This should be done as soon as possible after achieving
candidacy. And the list of final Dissertation Committee Members must be submitted to Rackham for APPROVAL
at least 6 months prior to the oral defense. The members of the Thesis Committee can form a valuable scientific
resource, and provide an opportunity for you to take advantage of the broad areas of expertise present at the
University of Michigan. In some cases, your research can be a collaboration among you, your main research
advisor, and another committee member. The composition of the thesis committee is subject to the approval of
the Biophysics Program Committee or Program Chair, as well as Rackham.
Additional meetings with the Thesis Committee may be requested by you, your research advisor, the Thesis
Committee, or the Biophysics Program Committee. At the very least, you should meet once a year; it is
recommended that you meet twice a year when approaching thesis defense.
The Biophysics Program has rules for the constitution of the Thesis Committee. These rules are consistent with
Rackham requirements, but they go beyond the general Rackham rules:
    1) The committee should consist of at least five members.
    2) Your thesis advisor/mentor is generally the Thesis Committee Chair. In some cases, there may be two
       Co-Chairs.
    3) A research scientist with an earned doctorate from an accredited institution can serve on the Thesis
       Committee. They can be the sole Thesis Committee Chair only if they have been so approved by
       Rackham and the Chair of the Biophysics program.
    4) At least three of the five committee members must be regular Academic Rackham Faculty members; i.e.,
       not Research Scientists. Two of these three should be chosen from the list of regular Biophysics program
       faculty members. One of these three must be other than a regular Biophysics faculty member.
These requirements also satisfy the requirements for those Biophysics graduate students who are in the Molecular
Biophysics Training Program; in that case, just be sure that at least three faculty members are also in the
Molecular Biophysics Program.

GOOD STANDING

It is critical to maintain a record of Good Standing in the Biophysics Graduate Program. Only students who are in
good standing are considered for financial support. The Rackham Graduate School’s definition of “Good
Standing” is detailed in the Rackham Handbook.

                                                       1 0
“Good Standing” in the Biophysics Graduate Program includes and supersedes the Rackham requirements and is
defined as

   a cumulative grade point average of “B” or better for all courses applied toward the degree program,
   passing grades in all courses applied toward the degree program, whether these courses can be defined as
    “cognates” or not,
   having entered into research with a Thesis Advisor affiliated with the Biophysics Graduate Program by spring
    term of the second year,
   maintaining satisfactory progress in dissertation research (Biophysics 990 and/or 995) with minimum grades
    of “S” as reported by the student’s Thesis Advisor, and
A student whose cumulative grade point average falls below a “B” in a given term or half-term will be placed on
probation for the following term or half term, or may be denied permission to register. See the Rackham
Handbook.

THESIS PREPARATION AND DEFENSE

Detailed instructions about the preparation and defense of the Dissertation are in the Dissertation Handbook,
available online at Rackham’s website. In general, the Dissertation is a comprehensive treatment of the Thesis
Research performed by the student. It is possible for the Dissertation to include material from journal articles
previously published by the student, however the Dissertation should also include contextual information
regarding the significance of the question being addressed, a discussion of other approaches used by previous
researchers, and the importance of the Thesis research.
Following the submission of the Dissertation to the Thesis Committee, the student must defend the Dissertation in
an oral presentation. The student must have a pre-defense meeting with the Office of Academic Records and
Dissertations at least 10 working days before the defense. The student can register online for this, and must be
registered to Defend and finish all requirements. The oral defense generally consists of an open presentation of the
thesis research to the University Community followed by a closed session with the Thesis Committee. At least
four members of the Thesis Committee must be present at the oral defense. Including the Chair or one Co-Chair
and Cognate Member. All members are required to read and comment on the submitted Dissertation before the
Defense.

VACATION POLICY & HOLIDAYS

Graduate students should discuss proposed vacation plans with their thesis advisor. For first year students, this
means your current rotation mentor and the Associate Chair for the Biophysics Graduate Program. Time between
semesters or academic quarters is considered an active part of the training period.

The University observes the following holidays:

       New Year’s Day
       Memorial Day
       Independence Day
       Labor Day
       Thanksgiving Day
       The day following Thanksgiving
       Christmas

University-designated holidays will be observed on the calendar day on which each falls except that holidays
falling on Sunday will be observed on the following Monday and holidays falling on Saturday will be observed on
the preceding Friday.


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STUDENT REPRESENTATION

The Biophysics program has annual elections in which they elect candidates to represent the graduate students for
the following:
     One student serves on the Admissions Committee (One year term)
     One student serves on the Curriculum Committee (One year term)
     One student serves as the Graduate Student Representative at the Biophysics faculty meetings (One year
         term)
MASTERS DEGREE

There is no independent Master of Science (M.S.) program in the Biophysics Graduate Program and the Program
will not admit students intending to obtain a terminal Master of Science Degree. However, the degree can be
granted in the extenuating cases of students who have unsuccessfully attempted to pass the preliminary
examination requirements. It can also be conferred as a non-terminal degree to students who are working to
complete the Ph.D. degree.
The Master of Science Degree in Biophysics, when granted by Biophysics Graduate Program, requires successful
completion of specific course requirements (4 courses in Physics and Chemistry, 2 courses in Biological
Chemistry, 1 course in Cell Biology, and 2 courses in Biophysics) with a minimum of 24 credit hours of course
work, average “B”, and 4 credit hours of cognate studies, passing grade “C-”. 990, 995 or “VI” courses can not
count towards this total – student should also see the Rackham Handbook section on Masters Degrees.


FINANCIAL INFORMATION

1.   POLICY ON FINANCIAL SUPPORT

The Biophysics Graduate Program is committed to seek continued support for your stipend, tuition, and health
insurance throughout your graduate training. To be eligible for such financial support, students must be in “Good
Standing” (see above). Students are expected to continue to make progress in their thesis research independent of
the source of their funding.
Financial support will be provided by Biophysics for full coverage of tuition and health care in your first year (12
months); in addition, a stipend in the amount of $25,553 is provided. Following the choice of a thesis mentor,
support will be provided by some mix of the following: (1) a Research Assistantship support by an individual
grant to the faculty member; (2) a Teaching Assistantship (GSI) in a relevant academic department; or (3) an
extramural fellowship.
Fellowship support may be in the form of a fellowship awarded directly to the student by a national agency (e.g.
NIH or NSF), or a research foundation or University Fellowship (e.g. Rackham Research Partnership, Rackham
Merit Fellowship, or Howard Hughes Fellowships) awarded on a competitive basis. In addition, the Molecular
Biophysics Training Grant Program, funded by the NIH, provides fellowship opportunities for U.S. citizens or
permanent residents. Participation in the Training Grant may require minor modifications in the curriculum.
These possibilities should be discussed with your Thesis Mentor and the Program office.
Fellowships usually carry a full tuition waiver. Graduate students holding at least a quarter-time appointment as a
Graduate Student Instructor (GSI) or Research Assistant (GSRA) will have the full tuition waived. However, you
will be liable for mandatory or registration fees, currently approximately $95 per term. Students in the Molecular
Biophysics Training Grant Program will have these fees waived.
Stipend Payment Schedules. Stipends for teaching, research and fellowship appointments are paid in equal
installments depending on whether the appointment is for a term or the academic year (e.g., four per term or
twelve per year). Students who have GSRA or GSI appointments are paid on the final day of the month. Students
who are on fellowship can expect their checks to be deposited somewhere in the middle of the month according to

                                                        1 2
the payment schedule of the Office of Financial Aid.

2.   LOANS

Loan funds administered through the Office of Financial Aid (2011 SAB) are available to meet the needs of any
educational expense for students while enrolled in the University. The need for this financial aid must be clearly
established by providing a complete statement of the applicant’s financial resources and expenses for the
academic year. Loans are NOT available for any non-education expense which is normally financed by a
commercial lending institution, nor are they available for the repayment of previously incurred indebtedness.
Short term loans up to $250 are considered by the Office of Financial Aid.
Departmental short term loans for emergencies are available. See the Student Services Administrator for details.

3.   INCOME TAX LIABILITY

Graduate Student Instructor stipends are currently considered remuneration for services performed and, as such,
are subject to withholding and income tax. Under the income tax law of 1986, stipends for Research Assistants,
fellowships and other forms of student aid are now subject to income tax. Current practice is subject to review by
the IRS and may change at any time. Consult with the district office where you file your income tax return for
interpretations of rules.




                                                        1 3
FACULTY AND INTERDISCIPLINARY PROGRAM FACULTY MEMBERS

    Name                        Department/s
    Al-Hashimi, Hashim          Biophysics, Chemistry
    Ballou, David               Biological Chemistry
    Banaszak Holl, Mark         Chemistry, Macromolecular Science & Engineering
    Bardwell, James             Biology
    Biteen, Julie               Chemistry
    Brooks, Charles             Chemistry, Biophysics
    Carlson, Heather A.         Medicinal Chemistry
    Chen, Zhan                  Chemistry
    Cierpicki, Tomasz           Pathology (Medical School)
    Fierke, Carol               Chemistry, Biological Chemistry
    Gafni, Ari                  Biophysics, Biological Chemistry
    Hunt, Alan                  Biomedical Engineering
    Joglekar, Ajit              Cellular & Developmental Biology
    Kerpolla, Tom               Biological Chemistry
    Kopelman, Raoul             Chemistry, Physics
    Kubarych, Kevin             Chemistry
    Lehnert, Nicolai            Chemistry
    Lei, Ming                   Biological Chemistry
    Lubensky, David             Physics
    Marsh, E. Neil              Chemistry
    Meiners, Jens-Christian     Biophysics, Physics
    Meyhöfer, Edger             Mechanical Engineering
    Ninfa, Alexander            Biological Chemistry
    Ogilvie, Jennifer           Biophysics, Physics
    Palfey, Bruce               Biological Chemistry
    Pecoraro, Vincent           Chemistry
    Penner-Hahn, James          Biophysics, Chemistry
    Raghavan, Malini            Microbiology & Immunology
    Ramamoorthy, Ayyalusamy     Biophysics, Chemistry
    Saper, Mark                 Biophysics, Biological Chemistry
    Savit, Robert               Physics
    Sension, Roseanne           Chemistry
    Sivaramakrishnan, Sivaraj   Cellular & Developmental Biology
    Skiniotis, Giorgios         Biological Chemistry
    Smith, Janet                Biological Chemistry
    Steel, Duncan               Biophysics, Physics, Engineering
    Sunahara, Roger             Pharmacology
    Swanson, Joel               Microbiology & Immunology
    Tesmer, John                Pharmacology
    Trievel, Ray                Biological Chemistry
    Veatch, Sarah               Biophysics
    Verhey, Kristen             Cellular & Developmental Biology, Life Sciences Institute
    Walter, Nils                Chemistry
    Wang, Shaomeng              College of Pharmacy
    Xu, Zhaohui                 Biological Chemistry
    Young, Matthew              Biological Chemistry, Bioinformatics
    Zand, Robert                Biological Chemistry, Macromolecular Science & Engineering
    Zochowski, Michal R.        Biophysics, Physics




                                         1 4
TYPICAL CHRONOLOGY OF PH.D. DEGREE


                                 Year 1
                                 Complete at least 4 courses.
                                 Two research rotations (Biophysics 890 – Fall and Winter terms).
                                 Initial preliminary exam(s).
                                 Select thesis mentor.
                                 Start thesis research.


                                 Year 2
                                 Complete remaining courses.
                                 Continue thesis research (Biophysics 990).
                                 Complete preliminary exams.
                                 Achieve Candidacy status.


                                 Year 3
                                 Continue thesis research (Biophysics 995).
                                 Select Thesis Committee (by late August).
                                 Present research prospectus.
                                 Present individual seminar.


                                 Year 4-5
                                 Continue thesis research (Biophysics 995).
                                 Annual report to committee.
                                 Dissertation defense.




COURSE REQUIREMENTS
All students must take a total of 6 courses, including the four core courses: Biophys 520 (Fall), Biophys 550
(Fall), Biophys 521 (Winter) and Biophysics 595 (Fall). The other 4 courses will be decided on in consultation
with your advisor (see below).

In the first year, you will also need to register for research rotations: Biophys 890 (Fall and Winter). In the second
year, when you’ve chosen an advisor, you’ll register for Biophys 990. These research courses – Biophys 890
and 990 – don’t count toward the 6 required courses.

Students with a background in Physics will probably need to take:
Biochemistry: Biolchem 550 (Fall)
Additional courses could be:
Cell Biology: MCDB 428 (Winter, Biological focus) or BiomedE 418 (Winter, Quantitative/Engineering focus)
Macromolecular Structure/Function: Chembio 501 (Fall) / Chembio 502 (Winter) or BiolChem 515 (Fall)
Dynamical Processes in Biophysics: Physics 417 (Winter)

                                                          1 5
Students with a background in Biology will need to obtain a solid background in Mechanics, Electricity and
Magnetism, Statistical/Thermal Physics, and Quantum Mechanics. Choose courses in your weakest area(s):
            Mechanics: Physics 401 (Fall or Winter – Intermediate Mechanics)
            E&M: Physics 405 (Fall or Winter – Intermediate Electricity and Magnetism)
            Statistical/Thermal: Chem 463/575 (Fall – Thermodynamics), or Chem 576 (Winter – Statistical
            Mechanics), or Physics 406 (Fall or Winter – Statistical and Thermal Physics)
            Quantum: Chem 461/570 (Fall or Winter – Physical Chemistry) or Physics 453 (Fall or Winter –
            Quantum Mechanics)

Once you’ve passed the prelims/chosen a lab, there are a number of courses related to specific areas of research,
which should probably be chosen after discussion with your advisor/thesis committee, for example:
            X-ray Crystallography: Biophys 602
            NMR: Biophys 503
            Kinetics: Chem 673
            Spectroscopy: Chem 580
And other courses in Math (463), Statistics (401), Bioinformatics, Applied Physics, etc.

Some suggested electives are listed below under “Course Descriptions.”


SAMPLE CURRICULUM
Physics Background
1st Fall:     Biophys 890
              Biolchem 515
              Biophys 520 (may be a challenge – find people to study with) or any necessary Physics
              Biophysics 550

1st Winter:        Biophys 890
                   Biophys 521
                   Cell Biology

2nd Fall:          Biophys 990
                   Biophys 520 if haven’t yet taken it and/or
                   Macromolecular Structure/Function or Research-related course or both
                   Biophys 595 if haven’t yet taken it

2nd Winter:        Biophys 990
                   Research-related course if haven’t yet taken 6 courses

Biochemistry Background
1st Fall:          Biophys 890
                   Biophys 520
                   Biophys 550
                   Quantum or Statistical/Thermal or other Physics

1st Winter:        Biophys 890

                                                          1 6
                           Biophys 521
                           Quantum or Statistical/Thermal or other Physics

2nd Fall:                  Biophys 990
                           Biophys 595 if haven’t yet taken it
                           More Physics if necessary or Research-related course or both

2nd Winter:                Biophys 990
                           Research-related course if haven’t yet taken 6 courses


COURSE DESCRIPTIONS
For more detailed and current information about courses please call the Student Services Administrator or check
the website of each department, or check the various course guides (i.e. LSA, Engineering) available online. In
many cases, a current short description of courses is maintained by the BGP Student Services Administrator.
LSA Course Guide: http://www.lsa.umich.edu/cg/
Engineering Course Guide: http://www.engin.umich.edu/students/current/academics/courses/
College of Pharmacy Course Guide: http://www.umich.edu/~pharmacy/students/courses.html
Biomedical Sciences Course Descriptions (in PIBS Curriculum Guide):
http://www.med.umich.edu/pibs/documents/pdf/2005CurriculumGuide.pdf


Department Affiliate                  Student Services           Email                              Phone        Website
                                      Administrator
                                      Beth Goodwin ...........................................
Biological Chemistry ................................            egoodwin@umich.edu                 764-8594     http://www.biochem.med.umich.edu/biochem/
Biomedical Eng……… Maria E. Steele...                             msteele@umich.edu                  647-1091     http://www.bme.umich.edu/
                                      Margarita Bekiares pappas@umich.edu
Chemistry ..................................................                                        764-7278     http://www.umich.edu/~michchem/
Chemical Biology……. Laura Howe                                   lkhowe@umich.edu                   763-7175     http://www.chembio.umich.edu/
Mathematics……                         Tara McQueen               tarac@umich.edu                    764-7436     http://www.math.lsa.umich.edu/
                                      Heidi Thompson             heiditho@umich.edu
Micro. & Immunology .............................. .......................................          647-6742     http://www.med.umich.edu/microbio/
                                      Mary Carr .................................................
Mol. Cell & Dev. Biol. ..............................            carrmm@umich.edu                   615-1635     http://www.mcdb.lsa.umich.edu/index.php
                                      Maria Herbel .............................................
Pharmacy ..................................................      mariamh@umich.edu                  615-6326     http://www.umich.edu/~pharmacy/index.html
                                      Christina Zigulis
Physics ......................................................   czigulis@umich.edu                 764-5539     http://www.lsa.umich.edu/physics/
                                      Michelle Melis
PIBS ..........................................................  msmtegan@umich.edu                 615-6538     http://www.med.umich.edu/pibs/index.html

The following courses illustrate the range of approved offerings at the time of the assembly of this handbook.
Some courses may have more detailed information than others. Courses change every year, be sure to contact the
Biophysics Student Services Office about their existence.
A.    BIOLOGICAL CHEMISTRY

      515.          Introductory Biochemistry. (3-4 hrs, Fall).
                    Prereq: 2 semesters of organic chemistry.
                    A one-term introductory biochemistry course that covers the biochemistry of the living state, the chemistry of amino acids, proteins, nucleic
                    acids, carbohydrates, lipids, and steroids, energy transformations and chemical reactions in living cells, function of immune system and
                    action of hormones, and self-regulation and self-replication of living organisms. Students may elect to participate in BIOLCHEM 491, a
                    weekly seminar presented jointly by clinicians and basic scientists, which correlates biochemistry lecture material with human disease
                    through the use of clinical case studies.
      550.          Protein Structure & Function. (3 hrs, Fall).
                    This course will relate protein structure to various aspects of protein function. The course will begin with a general introduction to three-
                    dimensional protein structure including discussion of structure determination methods and forces in protein structure and stability.
                    Significant sections of the course include (i) binding and allosterism, (ii) enzyme catalysis, (iii) protein-nucleic acid interaction, and (iv)
                    signal transduction and membrane proteins. The emphasis will be to relate details of structure to the function of the proteins discussed. The
                    course will include a molecular graphics component aimed at hands-on experience for the students.




                                                                                            1 7
     576.      Signal Transduction. (1 hr, Winter).
               Prereq: Biochem. 550 or 570; or permission of instructor.
               A review of hormone and neurotransmitter receptors as well as the cellular effectors that are regulated by receptor activation. Oncogene
               products as signal transducers and the interaction of the known signaling pathways are also covered. The various techniques used to study
               signal transduction as well as important experimental strategies employing these techniques will also be presented. Lecture.


B.   BIOMEDICAL ENGINEERING

     417.      [EECS 417.] Electrical Biophysics. (4 hrs, Fall).
               Prereq: EECS 211 or 314; [concurrently] EECS316.
               Electrical biophysics of nerve and muscle; electrical conduction in excitable tissue; quantitative models for nerve and muscle including the
               Hodgkin Huxley equations; biopotential mapping, cardiac electrophysiology, and functional electrical stimulation; group projects. Lecture
               and recitation.
     418.      Quantitative Cell Biology (4 hrs, Winter)
               Prerequisite: Biology 310, 311, Biochemistry 415, 451, 515, Physics 240, Math 216, Chemistry 130.
               This course introduces the fundamentals of cell structure and functioning. The goal is to provide a general background in cell biology, with
               emphasis placed on physical aspects that are of particular interest to engineers.
     525.      Cellular and Molecular Networks (3 hrs, Winter)
               Prerequisite: Biol 105 or Biol 112 and Math 215.
               This course is designed to equip the student with appropriate concepts and techniques for the quantitative analysis of the integrated behavior
               of complex biochemical systems. A general approach is developed from the basic postulates of enzyme catalysis and is illustrated with
               numerous specific examples, primarily from the microbial cell.


C.   BIOPHYSICS

     503.      Macromolecular NMR spectroscopy. (3 hrs).
               Prereq: Biophys 520/521, Bio.Chem 550 or 570, Chem 570.
               Quantum mechanical treatment of 1-D, 2-D and 3-D NMR, applied to biological macromolecules, mainly proteins. NMR pulse sequence
               design, data interpretation and structure calculations. Relaxation theory. Both solution and solid NMR will be treated.
     520.      Biophysical Chemistry I. (3 hrs, Fall).
               Prereq: Chem 575, and Bio.Chem 415 or Chem 451 or Chem 215.
               In general, permission of the course director.
               This course offers an overview of protein and nucleic acid structures. Intra- and inter-molecular forces, helix-coil transitions and protein
               folding will be treated in a thermodynamical context. Thermodynamics of solutions, configurational statistics, ligand interaction, multi-site
               interactions and cooperativity are treated in depth. Calorimetry and kinetics of protein ligand binding is discussed. Experimental and
               computational molecular dynamics.
     521.      Biophysical Chemistry II. (3 hrs, Winter).
               Prereq: Chem 570, and Bio.Chem 415 or Chem 215. In general, permission of the course director.
               This course gives the background and applications of several physical techniques used in biophysical research. General principles of
               spectroscopy will be explained. Macromolecular structure determination by X-ray diffraction and two-dimensional NMR will be treated in
               fair detail. IR, Raman, CD, EXAFS, EPR will be introduced. Electron, light and scanning microscopies and optical tweezers will be
               introduced. In addition, each instructor will be encouraged to give a demonstration of his technique in an informal setting.
     550.      Intro to Biophysics Lab. (3 hrs, Fall)
               This course teaches essential laboratory skills in Biophysics. Experiments cover sample preparation techniques, modern research methods
               and computational techniques. The final project will allow students to explore a topic of interest in greater depth.
     595.      Professional Development in Biophysics. (3 hrs, Fall)
               This course teaches professional skills such as writing research articles, reviews, grant proposals, and preparing and giving poster
               presentations and scientific talks. The scientific publishing process, including peer review, will be discussed and ethical rules and
               considerations explored. All students will draft an application for an NSF Graduate Fellowship.
     602.      Protein Crystallography: Principles of Macromolecular Crystallography (3 hrs, Winter)
               Prereq: Physical Chemistry
               Fundamental of the methods for determining 3-dimensional structures of large molecules by X-ray crystallography. Aimed at students who
               expect to use crystallography as a major tool for their research, and at those who want in-depth knowledge of the methods in order to
               analyze structure data.
     608.      Biophysical Principles of Microscopy. (3 hrs, on demand).
               Prereq: Physics 405; or permission of instructor.
               This course covers the fundamental physics and math behind modern microscopies, with applications in the biological/biochemical
               sciences. Included are phase, differential interference, fluorescence, confocal, 3-D imaging, scanning, and electron microscopies.
     801/802. Molecular Biophysics Seminar Series.
              Molecular Biophysics Training Grant students and non-trainees meet informally to discuss their research. As this seminar is taken for
              credit, students should register for it at the beginning of the semester. Non-trainee Biophysics students should register for 802.




                                                                           1 8
D.   CHEMISTRY

     451.   [Bio.Chem 451.] Introduction to Biochemistry I. (4 hrs, Fall)
            Prereq: Chem 215, Biol 152 or 195, and Math 115.
            This course is the first in a two-term sequence designed for students who are concentrators in biochemistry. Emphasis is on developing the
            capacity of the students to think about complex biological processes in terms of the underlying chemistry. An introductory section on
            proteins is followed by sections on enzymes and coenzymes. The discussion of biochemical energetics includes sections on glycolysis, the
            tricarboxylic acid cycle, electron transport, photosynthesis, and carbohydrate metabolism. The course has three lectures and one discussion
            per week. There are three hour exams and a final exam.
     452.   [Bio.Chem 452.] Introduction to Biochemistry II. (4 hrs, Winter).
            Prereq: Chem 451.
            This course is the second in a two-term sequence designed for students who are concentrators in biochemistry. Emphasis is on developing
            the capacity of the students to think about complex biological processes in terms of the underlying chemistry. Initially nucleic acids and
            nucleotides are discussed. The biosynthesis of amino acids and their utilization in cellular metabolism including protein synthesis serves as
            a primer for an introduction to biochemical genetics and virology.
     501.   Chemical Biology I (3 hrs, Fall)
            This course will provide a high-level overview on the structure, function and chemistry of biological macromolecules including proteins,
            nucleic acids and carbohydrates. Topics include protein and nucleic acid folding, energetics of macromolecular interactions (kinetics and
            thermodynamics), and mechanistic enzymology. Using specific examples from the current literature, each topic will stress how chemists
            have used molecular level tools and probes to help understand the specific systems under study. The over arching theme in this course will
            be that structure and function are intimately linked.
     502.   Chemical Biology II (3 hrs, Winter)
            This course is a continuation of CHEMBIO 501. The basic concepts obtained in CHEMBIO 501 will be applied to and demonstrated in
            three broad areas of interest to both chemists and biologists. The first topic will discuss combinatorial methods including SELEX and gene
            shuffling, combinatorial organic synthesis, high throughput screening and chemical genetics. The second topic will focus on signal
            transduction, emphasizing general concepts (at the molecular level) and how small molecules have been used to probe and modulate signal
            transduction pathways. The final topic will cover protein translation, stressing mechanistic aspects of protein synthesis and folding in vivo.
     555.   Molecular Modeling and Simulations. (3 hrs.)
            Familiarize students with some of the most important computational methods in the molecular sciences. Includes lecture-type presentations
            of scientific background of methods and computational laboratory using common software packages.
     570.   [461.] Molecular Physical Chemistry. (3 hrs, Fall & Winter).
            Prereq: Chem 260 (or 340), Phys 240, and Math 215.
            Chemistry 461 builds on the introduction to quantum mechanics that was given in Chemistry 260. Students will use the Schrödinger
            Equation in 1, 2, and 3-dimensions to solve exactly a series of important chemical problems including the harmonic oscillator, the rigid
            rotor, and the hydrogen atom. Group theory is introduced as an aid for understanding spectroscopic selection rules. Advanced spectroscopy,
            including transition probabilities, normal vibrational modes, and photoelectron spectroscopies are introduced and then used to deduce
            molecular structure. The valence-bond and molecular orbital theories of chemical bonding are discussed, and methods for performing
            quantum chemical calculations, including variational and perturbation methods, are introduced. The quantum mechanics of spin and angular
            momentum are discussed and used to interpret magnetic resonance spectra. NOTE: Students are strongly encouraged to elect the
            Computational Chemistry Laboratory (Chemistry 462, 1 credit) in the same term that Chemistry 461 is taken.
     575.   [463.] Chemical Thermodynamics. (3 hrs, Fall & Winter).
            Prereq: Chem. 461/462.
            This is the third of the three-term physical chemistry sequence Chemistry 260/461/463 and builds on material presented in both previous
            courses. The rigorous mathematical theory of classical thermodynamics will be developed, including applications to entropy, heat engines,
            solution properties, and phase and chemical equilibria. Modern statistical thermodynamics will be introduced. Modern theories of
            fundamental reaction rates will be used built on the phenomenological kinetics introduced in Chemistry 260. Methods for determining and
            understanding solid state structures will be discussed, building on group theory introduced in Chemistry 461.
     576.   Statistical Mechanics. (3 hrs. Winter)
            Prereq: Quantum mechanics
            Constitutes with 571 a full course for students specializing in physical chemistry. The foundation of equilibrium statistical mechanics and
            applications to problems of chemical interest. Included are discussions of imperfect gases and liquids, mixtures, solids, quantum statistics,
            surface chemistry and polymers.
     580.   Molecular Spectra and Structure. (3 hrs, Winter of odd years).
            Prereq: Chem 570.
            Review of atomic spectra; rotational, vibration-rotation, and electronic spectra of diatomic and simple polyatomic molecules; and deduction
            of molecular parameters from spectra. Role of symmetry and representation theory generally. Different spectroscopies from NMR, and EPR
            through ESCA.
     668.   Principles of Molecular Symmetry and Solid State Chemistry. (2 hrs, on demand).
            Prereq: Chem 570 or Solid-State Physics; or permission of instructor.
            Course will focus on basic surface phenomena which control the physical and chemical properties of extended surfaces. Introductions to a
            wide range of surface methods and issues regarding metal, semi-conductor and insulator surfaces will be discussed. Fundamental principles
            regarding the geometric and electronic structure of surfaces, surface thermodynamics, adsorption, desorption processes, surface diffusion,
            thermally induced surface reactions, state-specific reactions, and ion-surface interactions will be discussed. Current examples will also be
            discussed to indicate the current state of the art.




                                                                        1 9
     670.   Principles of Magnetic Resonance. (2 hrs, on demand).
            Prereq: Chem 570; or permission of instructor.
            Classical and quantum mechanical treatments of magnetic resonance phenomena. Included will be discussions of spin systems, rotating
            fields, electron-nucleus interactions, and relaxation phenomena. Experimental and theoretical aspects of nuclear magnetic resonance,
            electron spin resonance, and Fourier transform NMR; chemical shifts, spin-spin coupling, spin-orbit interactions, hyperfine interactions,
            spin-lattice relaxation, and other topics.
     673.   Mechanism and Kinetics. (3 hrs.)
            Prereq: BC550 or Chem 526/permission.
            This course will cover enzyme catalytic mechanisms and enzyme kinetics in depth. Ligand binding to macromolecules, transient kinetics,
            enzyme kinetics, kinetic isotope effects, structure-function analysis, protein structure, enzyme mechanisms and enzyme cofactors will be
            discussed. An emphasis will be placed on developing the key kinetic and thermodynamic concepts that govern the action of enzymes.
     711.   Metals in Biology and Medicine. (2 hrs.)


E.   MATHEMATICS

     404.   Intermediate Differential Equations. (3 hrs, Fall & Winter).
            Prereq: Math 216.
            This is a course oriented to the solutions and applications of differential equations. Numerical methods and computer graphics are
            incorporated to varying degrees depending on the instructor. There are relatively few proof s. Some background in linear algebra is strongly
            recommended.
     417.   Matrix Algebra I. (3 hrs, Fall & Winter).
            Prereq: 3 courses beyond Math 110.
            Many problems in science, engineering, and mathematics are best formulated in terms of matrices --- rectangular arrays of numbers. This
            course is an introduction to the properties of and operations on matrices with a wide variety of applications. The main emphasis is on
            concepts and problem-solving, but students are responsible for some of the underlying theory. Diversity rather than depth of applications is
            stressed.
     419.   Linear Spaces and Matrix Theory. (3 hrs, Fall & Winter).
            Prereq: 4 courses beyond Math 110.
            Math 419 covers much of the same ground as Math 417 (Matrix Algebra I) but presents the material in a somewhat more abstract way in
            terms of vector spaces and linear transformations instead of matrices. There is a mix of proofs, calculations, and applications with the
            emphasis depending somewhat on the instructor. A previous proof-oriented course is helpful but by no means necessary.
     425.   [Stat 425.] Introduction to Probability. (3 hrs, Fall & Winter).
            Prereq: Math 215 or 285.
            This course introduces students to useful and interesting ideas of the mathematical theory of probability and to a number of applications of
            probability to a variety of fields including genetics, economics, geology, business, and engineering. The theory developed together with
            other mathematical tools such as combinatorics and calculus are applied to everyday problems. Concepts, calculations, and derivations are
            emphasized.


     571.   Numerical Methods for Scientific Computing I (3 hrs. Fall & Winter)
            Prereq: MATH 214, 217, 417, 419, or 513; and one of MATH 450, 451, or 454
            Text (required): "Numerical Linear Algebra" by L.N. Trefethen and D. Bau (SIAM) From the preface to the text: "We hope the reader will
            come to share our view that if any other mathematical topic is as fundamental to the mathematical sciences as calculus and differential
            equations, it is numerical linear algebra." I hope students in this class will also come to share this view as I have. Math 571 is an
            introduction to numerical linear algebra, a core subject in scientific computing. Three types of problems are considered: (1) solving a
            system of linear equations, (2) computing eigenvalues and eigenvectors of a matrix, and (3) least squares problems. These problems often
            arise in applications in science and engineering, and many algorithms have been developed for their solution. However, standard approaches
            may fail if the size of the problem becomes large or if the problem is ill-conditioned, e.g. the operation count may be prohibitive or
            computer roundoff error may ruin the answer. We'll investigate these issues and study some of the accurate, efficient, and stable algorithms
            that have been devised to overcome these difficulties. The course grade will be based on homework, a midterm exam, and a final exam.
            Some homework exercises will require computing (Matlab is recommended). Topics: 1. vector and matrix norms, orthogonal matrices,
            projection matrices, singular value decomposition (SVD); 2. least squares problems, QR factorization, Gram-Schmidt orthogonalization,
            Householder triangularization, normal equations; 3. stability, condition number, backward error analysis, IEEE floating point arithmetic; 4.
            direct methods for Ax=b, Gaussian elimination, LU factorization, pivoting, Cholesky factorization; 5. eigenvalues and eigenvectors, Schur
            factorization, reduction to Hessenberg and tridiagonal form, power method, inverse iteration, shifts, Rayleigh quotient iteration, QR
            algorithm; 6. iterative methods for Ax=b, Krylov methods, Arnoldi iteration, GMRES, conjugate gradient method, preconditioning; 7.
            applications: image compression by SVD, least squares data fitting, finite-difference schemes for a two-point boundary value problem,
            Dirichlet problem for the Laplace equation


F.   MOLECULAR, CELL, & DEVELOPMENTAL BIOLOGY

     427.   Molecular Biology. (4 hrs, Fall & Winter).
            Prereq: Biol 305, and Biol 310 or 311.
            Lectures and discussions are concerned with the following topics: the physical methods used in molecular biology; structure and coding
            capacity of DNA chromosomes; DNA replication; transcription, protein synthesis; prokaryotic and eukaryotic regulation; molecular aspects
            of development; transposable elements and genetic engineering.



                                                                       2 0
     428.      Cell Biology. (4 hrs, Winter).
               Prereq: Biol 305, and Biol 310 or 311 or Bio.Chem 415.
               MCDB 428 is designed to provide students with a comprehensive overview of the biology of eukaryotes and prokaryotes at the cellular and
               molecular level. This course is intended for upper-level undergraduates and graduate students. The information is presented at a level that
               requires students to integrate information from their other biology, chemistry, and biochemistry courses.
               The following topics will be included: general techniques used in cell biology; general properties of membranes; secretion, endocytosis, and
               related processes; organelle biogenesis; signal transduction; lipoprotein metabolism; cytoskeleton and cell motility; cell cycle and its
               regulation; cell-cell and cell-matrix interactions; programmed cell death; functions of specialized cell types.
               Students will be expected to integrate the scientific data presented in class as well as to read and interpret basic research drawn from the
               current scientific literature. Grades will be based on three exams and the discussion section.
     514.      Topics in Molecular Evolution. (3 hrs, Winter alt).
               Prereq: Biol 305, and one upper-level course in either molecular or evolutionary biology; and permission of instructor.
               The subject of this course is methods of comparative DNA/amino acid sequence analysis using an evolutionary approach. Topics of
               sequence alignment and phylogeny reconstruction using DNA and protein sequences are covered.



G.   PHARMACEUTICAL CHEMISTRY

     758.      Methods of Computational Chemistry. (2 hrs, Fall).
               Prereq: [concurrently] Chem 468; or permission of instructor.
               A survey of those aspects of computer science most necessary to a practicing researcher in chemistry, particularly pharmaceutical
               chemistry. Main topics are chemical databases, molecular graphics, and conformational analysis. Two hours lecture a week and some
               practical exercises.


H.   PHYSICS

     401.      Intermediate Mechanics. (3 hrs, Fall & Winter).
               Prereq: Phys 126/128 or 240/241, and Math 216.
               This course is required for physics concentrators. It presents a systematic development of Newtonian mechanics beginning with single
               particle motion in one dimension and extending through multiparticle systems moving in three dimensions. The conservation laws of energy
               and linear and angular momentum are emphasized. Lagrangian mechanics is introduced, and Hamiltonian mechanics may be introduced as
               well. Physical systems treated in detail include the forced damped-oscillator, inverse square forced orbits, harmonic motion in two
               dimensions, coupled oscillations and rigid body motion in two and three dimensions. Mathematical topics given extensive treatment include
               vector algebra, elements of vector calculus, ordinary differential equations, plane and spherical polar coordinates and phasors and/or
               complex numbers. Grades are based on one or two hourly exams and a two-hour final.
     405.      Intermediate Electricity & Magnetism. (3 hrs, Fall & Winter).
               Prereq: Phys 126/128 or 240/241, and Math 216.
               This is a second course on the classical theory of electromagnetism. Familiarity with Maxwell’s equations at the level of 240 is assumed.
               Physics 340 is strongly recommended. The course elaborates on the theoretical content of the Maxwell theory as well as practical
               application. Topics: review of vector analysis; electrostatic boundary value problems; magnetostatics; dielectric and magnetic materials;
               Maxwell’s equations and electrodynamics; the wave equation, electromagnetic waves in free space, waves in conducting and dielectric
               media; guided waves; electromagnetic radiation, sources of EM radiation.
     406.      Statistical and Thermal Physics. (3 hrs, Fall & Winter).
               Prereq: Phys 126/128 or 240/241, and Math 216.
               An introduction to the thermal and other macroscopic properties of matter, their description in terms of classical thermodynamics, and their
               microscopic interpretation from the perspective of statistical mechanics. Techniques from classical mechanics, electricity and magnetism,
               and elementary quantum mechanics will be used. Frequent homework problem assignments, at least one hour exam, and a final examination
               will be given.
     411.      Introduction to Computational Physics. (3 hrs, Fall and Winter).
               Prereq: Phys 401, and Math 216, and some familiarity with a computer language.
               Introduction to techniques of computational physics with applications in optics, atomic, solid-state, nuclear and particle physics. Topics
               covered include motion in a force field, calculation of electric and magnetic fields, optical and ion-optical ray tracing, quantum-mechanical
               (QM) bound states (Schrödinger Equation) and QM barrier penetration and scattering.
     417.      [Chem 417.] Dynamical Processes in Biophysics. (3 hrs, Winter of even yrs).
               Prereq: Math 216, and Phys 340 or Chem 463 or 468.
               Topics include diffusion in biology. (electrical potentials across membranes, nerve action potentials, neuromuscular synapses, the physics of
               chemoreception, and reaction rate theory); optical techniques. (visible and ultraviolet light absorption, fluorescence and phosphorescence);
               and random processes in biophysics. (mathematics of random noise, membrane electrical fluctuations, quasielastic light scattering
               fluctuations, fluorescence fluctuations, and chaotic processes).
     453.      Quantum Mechanics. (3 hrs, Fall & Winter).
               Prereq: Phys 390.
               This course begins with an overview of the experimental and theoretical foundations for quantum mechanics. The theory is developed and
               applied to simple physical systems, with examples taken from atomic, molecular, condensed matter, nuclear, and particle physics. Topics
               include: basics of the Schrödinger equations and its solutions in rectangular and spherical coordinates; properties, uses, and interpretations
               of state functions; expectation values and physical observables; coherence, correlation, and interference. Other topics include spin, the
               exclusion principle, and some quantum statistical mechanics.



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I.   STATISTICS

     412.   Introduction to Probability and Statistics. (3 hrs, Fall & Winter).
            Prereq: [concurrently] Math 215 and CS 183.
            The objectives of this course are to introduce students to the basic ideas of probability and statistical inference and to acquaint students with
            some important data analytic techniques, such as regression and the analysis of variance. Examples will emphasize applications to the
            natural sciences and engineering. There will be regular homework, two midterms, and a final exam.




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