Pre-2005 rules - these rules apply only to students that joined the program before 2005

INITIAL PLANNING OF THE PROGRAM

THE WRITTEN PRELIMINARY EXAM AND THE GENERAL EXAMINATION

INITIAL PLANNING OF THE PROGRAM

Student's Background

Undergraduate majors for students in the Biophysics Program may vary from physics to math, to engineering, chemistry, biochemistry, biology and even biophysics. The number of courses taken depends partly on the student's background.

Students with backgrounds in physics, engineering and mathematics will need to learn some biology, chemistry and biochemistry. Conversely, students with backgrounds in biology may need to take some math (at least to differential equations) and also some physics and/or physical chemistry.

Students with backgrounds in chemistry (especially physical chemistry), biochemistry and biophysics have the most well-rounded background to take advanced courses immediately upon entering the program.

General Advice

Students in both divisions will need to know some biochemistry (which may mean learning organic chemistry). The reason for this is that biochemistry is the language of modern molecular and cellular biology. You need to know enough to speak the language. The specific courses will be determined by the level of knowledge and interest of the student. In addition, students interested in systems biophysics should know some physiology (either plant or animal).

All students should obtain expertise in either physics or physical chemistry to the level of a bachelor's degree. All students should have math to the level of differential equations.

All students should have some expertise in a field of biology. This may be gained by taking appropriate courses or otherwise familiarizing themselves with the systems with which they will be working.

All students should be computer literate by the time they take their general exams. This may involve either programming or learning to use programs (as for example, molecular modeling programs) written by others.

If a student is involved in using instrumentation, he/she should be familiar with the physics behind the method and understand the instrumentation at least well enough to talk to the technician.

Expertise in these areas can be obtained in several ways. A student may have obtained some of this knowledge as part of their baccalaureate degree. There may be courses the student will wish to take. Other knowledge may be obtained by reading, attending seminars or by interactions with other members of the research group. Any method can be used. The important part is that necessary skills be gained.

Initial Planning of the Program

Initial advising will be carried out by the Graduate Studies Chair or designee. One of the first questions asked of the student will be, "Are you interested in molecular or systems biophysics?" The answer to this question and the student's background will determine the first year program.

Students with a teaching assistantship are expected to take 2 courses + seminar. Students on a fellowship or research assistantship should take 3 courses. Number of courses rather than number of credit hours is specified because there is not necessarily a correlation between number of credit hours and the difficulty of a course. Students must also meet the minimum number of credit hours required by the Graduate School.

Divisions of the Biophysics Program

There are four main divisions of the Biophysics Program: Structural Biology and Molecular Biophysics, Cellular and Integrative Biophysics, Computational Biology and Molecular Biophysics and Biological Spectroscopy and Imaging. Any given research laboratory may have projects in more than one area of biophysics.

Course Requirements

All students must take one to two quarters of Introduction to Biophysics taught by the Biophysics Program.

Biophysics 702
All students must take two quarters of Introduction to Biophysics taught by the Biophysics Program.
Biochemistry
Students will be encouraged to take biochemistry (unless they have already had it). Some may need to take organic chemistry first. If you are admitted to this program, we encourage you to take organic chemistry before you arrive. This will greatly expedite your coursework. The level at which you will take biochemistry depends on your background and interests.
Other Classes
Other classes which can be taken include enzymes, proteins, membranes and many others. Students are also encouraged to improve their skills in math, physics, computer science, chemistry and biochemistry. Suggestions concerning these courses will be given elsewhere.
English
International students will be tested concerning English skills upon arrival and may be required to take written and/or spoken English.

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COMMITTEE SETUP

Advisor Selection
Unless the student is a fellowship recipient, he or she should select an advisor (or preceptor) no later than the end of the third quarter of residence. Fellowship winners have an additional quarter.

As part of the advisor selection process, the student should interview at least five members of the program and do at least three rotations. It is possible under some circumstances to select a preceptor who is not a member of the program.
Committee Selection
The advisory committee shall consist of three members in addition to the preceptor. At least two out of the four members of the committee must be members of the program. Committee members who are not members of the Biophysics Program must be approved by the Graduate Committee.
Function of the Committee
The purpose of the committee is to advise the student in his/her research and plan the student's program (See "The Contract", below). The committee will also function as members of the general examination committee.

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THE CONTRACT

Since the students in the program have diverse backgrounds and goals, it is not possible to have an exact set of degree requirements. Instead, the student and the committee decide on a set of requirements that will meet the student's goals. The program will be set up in the form of a contract between the student and the committee. The contract will include areas of expertise that the student should know, particular biological systems that the student should become familiar with and important biophysical methods. The contract may include courses that the student should take and books and articles that should be read. The reading list may either substitute for coursework or extend beyond the coursework. The contract is an interactive process between the student and the committee.

The student and advisor should begin formulating the contract soon after preceptor selection. The contract should be continuously updated as the student progresses through the curriculum. From time to time, the revised curriculum should be distributed to all members of the committee. As the student approaches the written preliminary exam, it should be specified in the contract the areas that will be the responsibility of each committee member. For purposes of the written preliminary exam, the scope of the contract will be narrowed to cover particular courses, books, etc. as the committee sees fit.

A copy of the final contract should be sent to the Graduate Committee for inclusion in the student's file no later than one quarter before the student will take his/her general exams. The final contract must be signed by the student and all members of the committee.

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THE WRITTEN PRELIMINARY EXAM AND THE GENERAL EXAMINATION

Before the end of the tenth quarter of residence, the student must complete both the written preliminary exam and the general exam.

The Written Preliminary Exam
The written preliminary exam is generally an open book exam. Each member of the committee will submit two questions to the student's advisor. The advisor may select one or both of the questions. The questions should be of such a nature as to examine the student's ability to think, solve problems and show that he/she has mastered the basic concepts of biophysics set out in the contract. The questions must concern material set out in the contract. The student must get all questions at once and will have seven days to take the exam. Occasionally, the student, committee member, and preceptor may decide that a certain question should be closed book.

The questions will be graded "high pass", "pass" and "fail". The student must obtain an average of "pass" on the exam and may not fail more than one section. If the committee wishes, numerical values (or ranges) may be assigned to "high pass", "pass" "fail" to expedite determining a final grade on the exam.

If a student passes the written preliminary exam, he/she will go on to the general exam proper. The time between completion of the written preliminary exam should not be more than one month (unless permission is obtained from the Graduate Studies Committee). If the student fails the written preliminary exam, it may be repeated upon recommendation of the committee.

Copies of the questions and answers for the Preliminary exam should be sent to the Graduate Committee for the student's file.
General Exams
The general exams will consist of a written and oral portion. The written portion will consist of a proposal and the oral portion will be the defense of that proposal.
- Written Portion of the General Exam
  1. The student will submit 4-5 possible topics to the adviser. The student and adviser will select one of these.
  2. The student will have two weeks to develop the proposal.
  3. The proposal will be submitted to the advisor who will have two weeks to read and make comments.
  4. The student will have one week to revise the proposal after which it will be submitted to the committee.
  5. The committee has one week to read and accept the proposal.
  6. The oral exam should be scheduled for no more than 3 weeks from the time that the committee receives the proposal.
  7. If the proposal is not accepted by the committee, the student will have two weeks to revise the proposal. If the proposal is not acceptable after this, the Graduate Committee must be notified.
  8. Topics. The topic may not be on the student's research. However, an exception can occasionally be made (with the full preapproval of the examination committee and grad studies chair). That is, in some cases graduate committees may choose to use this proposal as an evaluation of the creative potential of the student in his or her area of chosen research. However, this is only appropriate when the student's research is sufficiently removed from the research history and grant funding of the advisor's research. The deciding factor should rest on the extent to which the document reflects the sole creative efforts of the student. Therefore, it cannot fall within the specific aims of the current projects or history of the advisor or other scientists in the lab. It may be in the same area "i.e. proteins or membrane support" but should be on a different system ad use different techniques than the student is using in his/her research or has used in previous research. However, the topic should not be so far afield that the student can not write a proposal in two weeks and defend it (i.e. it is not a good idea to include cloning if you do not know anything about it).
  9. Contents. The proposal should be written like a grant proposal and include background, rationale, methods, expected results and difficulties that may be encountered. Adequate references including titles, first and last page numbers should be included.
  10. Copies of the proposal should be sent to the Graduate Committee for the student's file.
- General Exam
  1. A full two hours must be allowed for questions in the exam. The student may begin by presenting a very short (<10 min) summary of the proposal, but should be prepared with sufficient overheads or other visual aids to address any aspects of the proposal during the question period. The scope of the questions must be limited to (a) subjects mentioned in the proposal and (b) questions concerning deficiencies in the written preliminary exam. For example, if a student mentions molecular biology in the proposal, it is fair game. If it is not mentioned, the subject can not be explored. Hint: Most students have difficulty with simple topics such as pH. Also, students, please note that you probably know more about your proposal than committee members.
  2. The question as to how many transparencies the student may use has not been set by the program and is up to the discretion of the committee.
  3. The decision on the oral portion of the general exam must be unanimous. If the decision is to fail the student, then the committee may decide to allow the student to retake the exam. Please note that if a student fails a general exam twice, he/she can not be admitted to another Ph.D. program at this university.

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THESIS

The committee can be the same or different from that for the general exams.
Starting two years after passing the general exam, and no earlier than one year from the expected date of graduation, the committee should meet every six months to assess the progress of the student's research.
The defense of the thesis will consist of a 45 minute-1 hour seminar which is open to the public and should be well-advertised. The audience is encouraged to ask questions during this period. The public seminar is separate from the thesis defense, usually the day before.
For the thesis defense, the committee must be allowed to have a full two hours of questions. However, with the agreement of the committee, it may be advisable to have no more than a 30 minute presentation available at the beginning of the exam, during which faculty can ask questions.
By Graduate School rules, the student is considered to have completed the FINAL ORAL EXAMINATION successfully only when the decision of the Final Oral Examination Committee is unanimously affirmative.
Other rules of the Graduate School must be met.

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