GRADUATE STUDENT HANDBOOK

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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 you
rself
with requirements of the Biophysics p
rogram and the re
quirements 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), cell
ular 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
indepen
dent, 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 p
rogram to help students pr
epare 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 stude
nts intending to obtain a terminal Master of Science Degree.

Related information can be found on the Biophysics website
www.biop.lsa.umich.edu
.

T
his handbook
supersedes the website.


2

TABLE OF CONTENTS


WHERE TO GO FOR INFO
RMATION

................................
................................
..

3

DEPARTMENT STAFF

................................
................................
............................

4

CONTINUOUS ENROLLMEN
T POLICY
................................
...............................

5

GRADUATE SCHOOL REQU
IREMENTS

................................
.............................

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 INFORMATIO
N

................................
................................
...............

12

FACULTY AND ASSOCIAT
ED FACULTY MEMBERS
................................
......

14

TYPICAL CHRONOLOGY O
F 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



3

WHERE TO GO FOR INFORMATION


Graduate Student Handbook

This handbook is to b
e 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 a
nd the Rackham g
raduate 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
b
iophysics
-
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 4
th

floor

directly across from the Biophysics administrative
office (#4028)
. If you need to make copies that are course or lab related, s
top in the Administrative
Office and you will be given a code for the copy ma
chine.

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
loung
e

on the 4
th

floor

(room
4041)
.
Any mail addressed to you here in Biophysics
will be put there, as well as a
ny 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 Admini
strative Office (4028). You will find such information as
Fellowships, Scholarships, Grants offered, Job listings, and other University business pertaining to
graduate student
s
.



Graduate A
cademic Advisor


F
irst year students will see
Professor
Ayyalusamy

Ramamoorthy

for academic counseling
. After
your first year, your
Research Advisor/PI

will be your academic counselor
.



4

DEPARTMENT STAFF




Administration



Room

Telephone
*

Chair

Jens
-
Christian Meiners

4028C

4
-
1146

Associate

Chair
,

Graduate Program

Hashim Al
-
Hashimi

4022

5
-
3361

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

System
s

Administrator

Tony

Markel

4019

7
-
2146

Research
Engineer

Keith Shaw

3012

3
-
2501


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



5

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 t
hey 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_enrol
lment/
.


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 Poli
cy

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 dissertat
ion

by the Thesis Committee and

Rackham
, and
a final examination by
the Thesis Committee

7.

Minimum of four cognate credit hours


course
s

taken outside the Home Program. Undergraduate
transcripts/credentials need to have been submitted to Rackham within seve
n 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

Bio
physics 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 ter
m 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.


6

B
IOPHYSICS 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 b
iology 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.
P
re
-
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 Bioph
ysics 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 c
umulative
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 rul
es 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 suppleme
ntary 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. Yo
u 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
.
Th
is 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.


7

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 rec
onsideration
.

The student and the thesis m
entor are jointly responsible for following the Program and Graduate School
requirements for the Ph.D. The m
entor’s responsibilities begin at the time of his/her agreement to accept the
student for research. In
addition to

supervising the research, the thesis m
entor 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
Bioc
hemistry/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 Classi
cal 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. Th
ese three parts can be taken and
passed independently of each other.


The Biochemistry/Cell Biology and the Physics/Physical Chemistry part
s

will be given in the

winter

term
. It is

recommended that students with the appropriate undergraduate background tak
e 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 e
xam 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 p
reliminary list of topics to be covered by the exams is included below:


Biochemis
try 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


8



Michaelis
-
Menten



Types of inhibition



Mechanisms



Regulation



Lipids

o

Triglycerides

o

Phospholipids

o

Steroids

o

Membranes



Carbohydrates

o

Glycolysis

o

Gluconeogenesis

o

Glycogen

o

Cit
ric 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


9

o

Phase transitions

o

Boltzmann dist
ribution


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 inf
ormation 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 origina
l 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 pr
oposal.


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 R
esearch Proposal to the Graduate Chair no later than the middle of their 4
th

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 Propos
al 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 backgr
ound 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.
Cand
idates 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 4
th

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 4
th

semester.

4.

The 1 month grace period (May) for Prelims is for students

who are registered full time the previous Fall

and Winter
ter
ms.

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 th
e 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 enc
ouraged to accept these invitations as they help develop good communication skills.


1 0

I n a d d i t i o n t o
p r e s e n t i n g

a s e m i n a r, a l l s t u d e n t s a r e
r e q u i r e d
t o a t t e n d t h e B i o p h y s i c s S e m i n a r S e r i e s. T h e s e r i o u s
s t u d e n t w i l l t a k e a d v a n t a g e o f a l l l e a r n i n g o p p o r t u n i t i
e s, a n d t h e S e m i n a r S e r i e s r e p r e s e n t s e x c e l l e n t s o u r c e s o f
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 obtai
ned Candidacy, your main activity in Biophy
sics will be thesis
research.
Every semester y
ou 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 COMM
ITTEE

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.
T
he members of the Thesis Committee can form a valuable scientific
resource, and provide an opportunity for you to take advantag
e 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 ap
proval of
the Biophysics Program Committee or Program Chair, as well as
Rackham
.

Additional meetings with the Thesis Committee may be reques
ted by you, your research adviso
r, the Thesis
Committee, or the Biophysics Program Committee. At the very least, yo
u 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 beyo
nd the general Rackham rules:

1)

The committee should consist of at least five members.

2)

Your thesis adviso
r
/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 accre
dited 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 R
ackham Faculty members;
i.e.
,
not Research Scientists. Two of these three should be chosen from the list of
regular

Biophysics program
f
aculty members. One of these three must be
other

than a regular Biophysics f
aculty member.

These requirements also sat
isfy 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 1

“ G o o d
S t a n d i n g ” i n t h e B i o p h y s i c s G r a d u a t e P r o g r a m i n c l u d e s a n d s u p e r s e d e s t h e R a c k h a m r e q u i r e m e n t s a n d i s
d e f i n e d a s



a c u m u l a t i v e
g r a d e p o i n t a v e r a g e

o f “ B ” o r b e t t e r f o r a l l c o u r s e s a p p l i e d t o w a r d t h e d e g r e e p r o g r a m,



p a s s i n g g r a d e s

i n
a l l c o u r s e s a p p l i e d t o w a r
d t h e d e g r e e p r o g r a m, w h e t h e r t h e s e c o u r s e s c a n b e d e f i n e d a s
“ c o g n a t e s ” o r n o t,



h a v i n g e n t e r e d i n t o r e s e a r c h w i t h a T h e s i s
A d v i s o r

a f f i l i a t e d w i t h t h e B i o p h y s i c s G r a d u a t e P r o g r a m b y s p r i n g
t e r m o f t h e s e c o n d y e a r,



m a i n t a i n i n g s a t i s f a c t o r y p r o g r e s s i n d i s s
e r t a t i o n r e s e a r c h ( B i o p h y s i c s 9 9 0 a n d/o r 9 9 5 ) w i t h m i n i m u m g r a d e s
o f “ S ” a s r e p o r t e d b y t h e s t u d e n t ’ s T h e s i s
A d v i s o r
, a n d

A s t u d e n t w h o s e c u m u l a t i v e g r a d e p o i n t a v e r a g e f a l l s b e l o w a “ B ” i n a g i v e n t e r m o r h a l f
-
t e r m w i l l b e p l a c e d o n
p r o b a t i o n f o r t h e f o l l
o w i n g t e r m o r h a l f t e r m, o r m a y b e d e n i e d p e r m i s s i o n t o r e g i s t e r. S e e t h e R a c k h a m
H a n d b o o k
.


T H E S I S P R E P A R A T I O N A N D D E F E N S E

D e t a i l e d i n s t r u c t i o n s a b o u t t h e p r e p a r a t i o n a n d d e f e n s e o f t h e D i s s e r t a t i o n a r e i n t h e
D i s s e r t a t i o n H a n d b o o k
,
available
online at R
ackham’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 Dis
sertation should also include contextual information
regarding the significance of the question being addressed, a discussion of other approaches used by previous
researchers, and the import
ance of the Thesis research.

Following the submission of the Disse
rtation to the Thesis Committee, the student must defend the Dissert
ation 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
d
efense
. The student ca
n register online for this
,

a
nd 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 b
e present at the oral defense. Including the Chair or one Co
-
Chair
and Cognate Member.
All members are required to read and commen
t on the submitted Dissertation before the
Defense.

VACATION POLICY

& HO
LIDAYS

Graduate students should
discuss
proposed
vacation plans
with their thesis adviso
r
.
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 holida
ys 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.


1 2

S T U D E N T R E P R E S E N T A T I O N

T h e
B i o p h y s i c s
p r o g r a m

h a s a n n u a l e l e c t i o n s i n w h i c h t h e y e l e c t c a n d i d a t e s t o r e p r e
s e n t t h e
g r a d u a t e
s t u d e n t s
f o r
t h e f o l l o w i n g:



O n e s t u d e n t s e r v e s o n t h e A d m i s s i o n s C o m m i t t e e ( O n e y e a r t e r m )



O n e s t u d e n t s e r v e s o n t h e
C u r r i c u l u m

C o m m i t t e e ( O n e y e a r t e r m )



O
n e s t u d e n t

s e r v
e s a s t h e G r a d u a t e S t u d e n t R e p r e s e n t a t i v e

at

the Biophysics

faculty meetings (One year
term)

MASTERS DEGREE

There is
no

ind
ependent Master of Science (M.S
.) program in the Biophysics Graduate Program and the Program
will not admit students intending to obt
ain 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 stud
ents 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 Bio
logical
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,
99
5 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 you
r 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 wil
l 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 awar
ded 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
perm
anent residents
. Participation in the Training Grant may require minor modifications in the curriculum.
These possibilities shou
ld 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 th
e 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 fo
r 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 yea
r)
.

Students who have GSRA or GSI appointments are paid on the fin
al 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 3

t h e p a y m e n t s c h e d u l e o f t h e O f f i c e o f F i n a n c i a l A i d.

2.

LOANS

Loan funds administered through the Office of Financia
l 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 t
o $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 remun
eration 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 subje
ct 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 4

F A C U LT Y A N D
I N T E R D I S C I P L I
N A R Y P R O G R A M

F A C U LT Y ME MB E R S


N a m e

D e p a r t m e n t/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 Chemistr
y

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 5

T Y P I C A L C HR O N O L O G Y O F P H.D. D E G R E E


Y e a r 1

C o m p l e t e
a t l e a s t
4 c o u r s e s.

T w o r
e s e a r c h r o t a t
i o n s ( B i o p h y s i c s 8 9 0


F a l l a n d W i n t e r t e r m s
).

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 t
hesis research (Biophysics 995).

Select Thesis Committee (by late
August).

Present research prospectus.

Present individual seminar.


Year 4
-
5

Continue t
hesis research (Biophysics 995).

Annual report to
c
ommittee.

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 co
nsultation
with your advisor (s
ee be
low
)
.


In the first year, you will also need to register for research rot
ations: 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 6


S t u d e n t s w i t h a
b a c k g r o u n d i n B i o l o g y

w i l l n e e d t o o b t a i n a s o l i d b a c k g r o u n d i n M e c h a n i c s, E l e c t r i c i t y a n d
M a g n e t i s m, S t a t i s t i c a l/T h e r m a l P h y s i c s, a n d Q u a n
t u m M e c h a n i c s. C h o o s e c o u r s e s i n y o u r w e a k e s t a r e a ( s ):


M e c h a n i c s
:
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.


S
ome s
uggested

electives are listed below

under “Course Descriptions
.


SAMPLE CURRICULUM


Physics Background

1
st

Fall:

Biophys 890



Biolchem 515



Biophys 520 (may be a challenge


find people to study

with) or
any necessary

Physics



Biophysics 550


1
st

Winter:

Biophys 890



Biophys 521



Cell Biology


2
nd

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


2
nd

Winter:

Biophys 990



Research
-
related course if haven’t yet taken 6 courses


Biochemistry Background

1
st

Fall:


Biophys 890



Biophys 520



Biophys 550



Quantum or Statistical/Thermal or other Physics


1
st

Winter:

Biophys 890


1 7



B i o p h y s 5 2 1



Q u a n t u m o r S t a t i s t i c a l/T h e r m a l o r o t h e r P h y s i c s


2
nd

Fall:


Biophys 990



Biophys 595 if haven’t yet taken it



More Physics if necessary or Research
-
rel
ated course or both


2
nd

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 de
partment
,

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 Admini
strat
or.

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

Administrator

Email

Phone

Website

Biological Chemistry
................................
.


Beth Goodwin

................................
............


egoodwin@umich.edu

764
-
8594

http://www.biochem.med.umich.edu/biochem/

Biomedical En
g………

Maria E. Steele
...

msteele@umich.edu

647
-
1091

http://www.bme.umich.edu/

Chemistry

................................
..................


Margarita Bekiares

pappas
@umich.edu

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/

Micro. & Immunology

..............................


Heidi Thompson

................................
........


heiditho
@umich.edu

647
-
6742

http://www.med.umich.edu/microbio/

Mol. Cell &
Dev. Biol.

..............................


Mary Carr
................................
...................


carrmm@umich.edu

615
-
1635

http://www.mcdb.lsa.umich.edu/index.php

Pharmacy

................................
...................


Maria Herbel

................................
..............


mariamh
@
umich.edu

615
-
6326

http://www.umich.edu/~pharmacy/index.html

Physics
................................
.......................


Christina Zigulis

czigulis@umich.edu

764
-
5539

http://www.lsa.umich.edu/physics/

PIBS
................................
...........................


Michelle Melis

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).

Prere
q: 2 semesters of organic chemistry.

A one
-
term introductory biochemistry course that covers the biochemistry of the living state, the chemistry of amino acids, protein
s, nucleic
acids, carbohydrates, lipids, and steroids, energy transformations and chemi
cal 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 sci
entists, 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 w
ill begin with a general introduction to three
-
dimensional protein structure including discussion of structure determination methods and forces in protein structure and sta
bility.
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 protein
s discussed. The
course will include a molecular graphics compo
nent aimed at hands
-
on experience for the students.


1 8

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 u
sed to study
signal transduction as well as important experimental strategies employing these tec
hniques 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; quant
itative models for nerve and muscle including the
Hodgkin Huxley equations; biopotential mapping, cardiac electrophysiology, and functional electrical stimulation; group proje
cts. Lecture
and recitation.

418.

Quantitative Cell Biology

(4 hrs, Winter)

Prerequisi
te: Biology 310, 311, Biochemistry 415, 451, 515, Physics 2
40, Math 216, Chemistry 130.

This course introduces the fundamentals of cell structure and functioning. The goal is to provide a general background in cel
l biology, with
emphasis placed on physica
l 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 qua
ntitative analysis of the integrated behavior
of complex biochemical systems. A general approach is developed from the basic postulates of enzyme catalysis and is illustra
ted with
numerous specific examples, primarily from the microbial cell.


C.

BIOPHYSICS

5
03.

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 interpretat
ion 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 i
nteraction, multi
-
site
interactions and cooperativity are treated in depth. Calorimetry and kinetics of protein ligand binding is discussed. Experim
ental and
computational molecular dynamics.

521.

Biophysical Chemistry II
. (3 hrs, Winter).

Prereq: Chem 57
0, 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. Macromolec
ular 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 wi
ll be
introduced. In addition, each in
structor 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 resea
rch 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 r
ules and
considerations explored. All students will draft a
n 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/biochemic
al
sciences. Included are phase, differential interference, fluorescen
ce, confocal, 3
-
D imaging, scanning, and electron microscopies.

80
1/80
2
.

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, stu
dents should register for it at
the beginning of the semester
.

Non
-
trainee Biophysics students should register for 802
.



1 9

D.

CHEMISTRY

451.

[Bio.Chem 451.]
Introduction to Biochemistry I
. (4 hrs, Fall)

Prereq: Chem 215, Biol 152 or 195, and Math 115.

This cou
rse 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 se
ction on
proteins is followed by sections on enzymes and coenzymes. The discussion of biochemical energetics includes sections on glyc
olysis, the
tricarboxylic acid cycle, electron transport, photosynthesis, and carbohydrate metabolism. The course has thre
e 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 concen
trators in biochemistry. Emphasis is on developing
the capacity of the students to think about complex biological processes in terms of the underlying chemistry. Initially nucl
eic acids and
nucleotides are discussed. The biosynthesis of amino acids and the
ir 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 interact
ions (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 ove
r 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 demonstrate
d 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 modul
ate signal
transduction pathways. The final topic will cover protein translation, stressing mechanistic aspec
ts 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 backgrou
nd

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 w
as 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 a
s an aid for understanding spectroscopic selection rules. Advanced spectroscopy,
including transition probabilities, normal vibrational modes, and photoelectron spectroscopies are introduced and then used t
o 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 us
ed 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 kinetic
s 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, qua
ntum st
atistics,
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; a
nd 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. Introd
uctions 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, surfa
ce diffusion,
thermally induced surface reaction
s, state
-
specific reactions, and ion
-
surface interactions will be discussed. Current examples will also be
discussed to indicate the current state of the art.


2 0

670.

Principles of Magnetic Resonance
. (2 hrs, on demand).

Prereq: Chem 570; or permission of i
nstructor.

Classical and quantum mechanical treatments of magnetic resonance phenomena. Included will be discussions of spin systems, r
otating
fields, electron
-
nucleus interactions, and relaxation phenomena. Experimental and theoretical aspects of nuclea
r 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 enzy
mes.

711.

Metals in Biology and Medicine.

(2

hrs.
)


E.

MATHEMATICS

404.

Intermediate Differen
tial 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 graphic
s 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 o
f 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 empha
sis 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 pr
esents 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 applicatio
ns 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 to
gether 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 re
ader will
come to share our view that if any other mathematical topic is as fundamental to the mathematical sciences as calculus an
d differential
equations, it is numerical linear algebra." I hope students in this class will also come to share this view as I have. Math 5
71 is an
introduction to numerical linear algebra, a core subject in scientific computing. Three types of problems a
re considered: (1) solving a
system of linear equations, (2) computing eigenvalues and eigenvectors of a matrix, and (3) least squares problems. These pro
blems 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 iss
ues 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 fina
l 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 eigenve
ctors, 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, preconditionin
g; 7.
applications: i
mage 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).

Prer
eq: Biol 305, and Biol 310 or 311
.

Lectures and discussions are concerned with the following topics: the physical methods used in molecular biology; structure a
nd coding
capacity of DNA chromosomes; DNA replication; transcription, protein synthesis; proka
ryotic and eukaryotic regulation; molecular aspects
of development; transposable elements and genetic engineering.


2 1

4 2 8.

C e l l B i o l o g y
. ( 4 h r s, W i n t e r ).

P r e r e q: B i o l 3 0 5, a n d B i o l 3 1 0 o r 3 1 1 o r B i o.C h e m 4 1 5.

M C D B 4 2 8 i s d e s i g n e d t o p r o v i d e s t u d e n t s w i t h a c o m p r e
h e n s i v e o v e r v i e w o f t h e b i o l o g y o f e u k a r y o t e s a n d p r o k a r y o t e s a t t h e c e l l u l a r a n d
m o l e c u l a r l e v e l. T h i s c o u r s e i s i n t e n d e d f o r u p p e r
-
l e v e l u n d e r g r a d u a t e s a n d g r a d u a t e s t u d e n t s. T h e i n f o r m a t i o n i s p r e s e n t e d a t a l e v e l t h a t
r e q u i r e s s t u d e n t s t o i n t e g r a t e i n f
o r m a t i o n f r o m t h e i r o t h e r b i o l o g y, c h e m i s t r y, a n d b i o c h e m i s t r y c o u r s e s.

T h e f o l l o w i n g t o p i c s w i l l b e i n c l u d e d: g e n e r a l t e c h n i q u e s u s e d i n c e l l b i o l o g y; g e n e r a l p r o p e r t i e s o f m e m b r a n e s; s e c r e t i o n, e
n d o c y t o s i s, a n d
r e l a t e d p r o c e s s e s; o r g a n e l l e b i o g e n e s i s; s i
g n a l t r a n s d u c t i o n; l i p o p r o t e i n m e t a b o l i s m; c y t o s k e l e t o n a n d c e l l m o t i l i t y; c e l l c y c l e a n d i t s
r e g u l a t i o n; c e l l
-
c e l l a n d c e l l
-
m a t r i x i n t e r a c t i o n s; p r o g r a m m e d c e l l d e a t h; f u n c t i o n s o f s p e c i a l i z e d c e l l t y p e s.

S t u d e n t s w i l l b e e x p e c t e d t o i n t e g r a t e t h e s c i e n t
i f i c d a t a p r e s e n t e d i n c l a s s a s w e l l a s t o r e a d a n d i n t e r p r e t b a s i c r e s e a r c h d r a w n f r o m t h e
c u r r e n t s c i e n t i f i c l i t e r a t u r e. G r a d e s w i l l b e b a s e d o n t h r e e e x a m s a n d t h e d i s c u s s i o n s e c t i o n.

5 1 4.

T o p i c s i n M o l e c u l a r E v o l u t i o n
. ( 3 h r s, W i n t e r a l t ).

P r e r e q: B i o l 3 0 5
, a n d o n e u p p e r
-
l e v e l c o u r s e i n e i t h e r m o l e c u l a r o r e v o l u t i o n a r y
b i o l o g y
; a n d p e r m i s s i o n o f i n s t r u c t o r.

T h e s u b j e c t o f t h i s c o u r s e i s m e t h o d s o f c o m p a r a t i v e D N A/a m i n o a c i d s e q u e n c e a n a l y s i s u s i n g a n e v o l u t i o n a r y a p p r o a c h. T o p i c s
o f
s e q u e n c e a l i g n m e n t a n d
p
h y l o g e n y

r e c o n s t r u c t i o n u s i n g D N A a n d p r o t e i n s e q u e n c e s a r e c o v e r e d.


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 scie
nce 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.

In
termediate 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 dimens
ion 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 introduc
ed as
well. Physical sy
stems 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 treat
ment include
vec
tor 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 & Magnetis
m
. (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 co
urse 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 magneti
c materials;
Maxwell’s equations and electrod
ynamics; 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 2
40/241, and Math 216.

An introduction to the thermal and other macroscopic properties of matter, their description in terms of classical thermodyna
mics, and their
microscopic interpretation from the perspective of statistical mechanics. Techniques from cla
ssical mechanics, electricity and magnetism,
and elementary quantum mechanics will be used. Frequent homework problem assignments, at least one hour exam, and a final exa
mination
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, Win
ter 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); o
ptical techniques. (visible and ultraviolet light absorption, fluorescence and phosphorescence);
and random processes in biophysics. (mathematics of random noise, membrane electrical fluctuations, quasielastic light scatte
ring
fluctuations, fluorescence fl
uctuations, 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 deve
loped and
applied to simple physi
cal 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, an
d interpretations
of state functions; expectation values and physical observables; coherence, correlation, and interference. Other topics inclu
de spin, the
exclusion principle, and some quantum statistical mechanics.


2 2


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 ac
quaint students with
some important data analytic t
echniques, 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.