Page Contents:
- Research Focus
- Course Requirements
- Seminar Requirements
- Course Load
- Grades
- Other Requirements
- Progress Evaluation
- Preliminary Examination
- Progress Reports
- Warrants
- Dissertator Status
- Thesis and Final Exam
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Proposed structure of active and inactive CooA with detail of heme environment from the CooA crystal structure (image courtesy of J. Burstyn)
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Biophysics Handbook
Overview
The doctor of philosophy degree with a major in Biophysics is an interdepartmental offering under the supervision of the Biophysics program committees. Although a master's degree may be conferred through the program, students are not admitted for study toward a terminal master's degree. The Biophysics degree is intended for those who wish to emphasize physical principles and methods in solving biological problems. Graduate students in Biophysics have a wide range of research topics from which to select for advanced research and training; these topics include biomolecular structure and function interactions, protein engineering and biotechnology, virus structure and function, enzyme catalysis and kinetics, membranes, neurochemistry, and electrophysiology. Normally work for the Ph.D. degree requires four to six years total time in graduate school for candidates who enter with few deficiencies.
A. Research Focus back to top
The candidate is encouraged to begin research as quickly as possible since it is research experience that brings focus and meaning to the classroom studies and since research progress provides judgment and self-confidence for independent work. A student may arrange by agreement with a selected major professor to enter the program and begin study directly in the thesis laboratory. More frequently, the student will enter unassigned and must select a thesis laboratory and major professor by the end of the first semester of graduate study. To guide this decision, an introduction and overview of the research expertise of each Biophysics faculty member is provided through this website and during an orientation session for new students. During the first semester, laboratory rotations (in up to three laboratories) are arranged by agreement with participating faculty to acquaint the student with the research in a potential thesis area. The student is encouraged to arrange rotations that provide exposure to a variety of fields, research methodologies and laboratory cultures. Financial assistance is provided through the Biophysics program during the period of first semester laboratory rotations. Once a thesis lab and major professor has been selected, financial assistance in the form of stipend support becomes the responsibility of the major professor.
B. Course Requirements back to top
The program is flexible in its formal course requirements and emphasizes excellence in research. Course work for the degree in Biophysics is selected primarily from the offerings of the various departments of the faculty. Course requirements are considered separately for each candidate and will take into account the needs, interests, and preparation of the candidate. Minimally, the Ph.D. requires 32 graduate-level credits to be completed as a graduate student at the UW-Madison.
Currently, the Graduate Program in Biophysics has a Core Curriculum of four recommended courses (each student normally will take at least three of these core courses):
Biochemistry 601 (2 cr) Protein and Enzyme Structure and Function
Biochemistry 612 (3 cr) Prokaryotic Molecular Biology (cross-listed with Genetics, Bact.)
Chemistry 665 (4 cr) Biophysical Chemistry (cross-listed as Biochem 665)
Physiology 610 (4 cr) Cellular and Molecular Neuroscience (cross-listed with Neurosci, Phmcol-M)
Specialty Courses are elected to focus expertise and complement a student’s research training.
C. Seminar Requirements back to top
All Biophysics graduate students are required to register for and attend a seminar course each semester in an area relevant to biophysics and to give at least one oral presentation each year in these courses. The seminar courses generally examine the current research literature in a particular area of focus. The traditionally recommended course has been Biochemistry 905, Biomolecular Structure, team-taught and led by Ivan Rayment. Other seminars have been selected and approved in semesters when the topic is of particular interest to a student. In an exciting new development beginning with the fall 2005 semester, a new seminar option, Chem 872, Topics in Biophysics was designed and offered in response to a need for greater breadth in the coverage of topics relevant to biophysics. It is anticipated that this seminar will continue as an important vehicle for bringing together the biophysics community of students and faculty since as the topics vary each semester different faculty will be called on to lead the topical units.
D. Course Load back to top
Candidates must register for a full time credit load in the fall and spring semesters. A full time load is 8 - 12 credits per semester (including courses and research); generally, the maximum credit load is recommended apportioned between courses, seminar and research. The summer course load can be as low as 2 credits (usually research), or 3 credits once the student has achieved dissertator status. During the first semester, the student registers for research credits (990 course) in the department of the Biophysics Program Director. The number of research credits is selected to bring the total course and research credits to a full time load (typically this is 3 or more 990 research credits). Upon choosing a laboratory, the 990 research credits are registered under the department of the major professor.
E. Grades back to top
In addition to the Graduate School requirement that the overall grade point average (GPA) of non-research courses be 3.0 (B average) or better, a candidate for the Ph.D. degree in Biophysics must achieve a cumulative biophysics grade point average (GPA) of 3.0 (B) or better in the core and specialty courses. Grades in research, advanced conference and seminar courses are not included in the Biophysics GPA.
A candidate who obtains a grade of C or lower in one of the core or specialty courses must repeat the course and obtain a grade of BC or better. In such cases both grades (original and repeat) are averaged in the Biophysics GPA.
Credits are not counted from courses in which a grade of C or below was obtained. The course may be taken again to achieve a higher grade, or another course can be substituted to obtain the needed credits.
F. Other Requirements back to top
Teaching requirements: None
Foreign language requirement: None
Minor: Because of the interdisciplinary nature of the Graduate Program in Biophysics, the Graduate School does not require a minor. Students are encouraged, however, to take courses in areas such as biotechnology, computer science, electrical and computer engineering, molecular biology, or physics as appropriate to their individual training goals.
G. Progress Evaluation back to top
Each summer the Examination and Certification Committee reviews the academic performance of all students in the Biophysics Program. On the Committee’s recommendation a candidate may be dropped from the Program if the student's academic performance is unsatisfactory. A biophysics GPA below 3.0 can constitute grounds for probation (one year at this level) or dropping (more than one year at this level). Other grounds for dropping a student from the program are: failure to pass the preliminary examination in a timely fashion, failure to take the required course load, or poor research productivity. The progress of students who have not passed the preliminary examination by the end of the fifth semester or who have spent more than five years in the Program will be monitored individually by the Examination and Certification Committee in consultation with the candidate's Advisory Committee; written recommendations will be made to the biophysics faculty for their consideration.
H. Preliminary Examination (Written and Oral) back to top
A certification form (available from the Biophysics Office and listed below) is to be filled out by each second-year candidate and the candidate's major professor at the beginning of the fall semester. The certification form lists: (1) relevant courses taken, (2) other educational experiences, (3) research projects undertaken, and (4) the courses and other educational experiences to be completed to satisfy the formal Ph.D. requirements (excluding research and thesis). This certification form is signed by the major professor and is sent to the Examination and Certification Committee for their consideration.
Certification Form (pdf format)
Certification Form (Word document)
At this time the student and major professor choose two faculty members (in addition to the major professor) to serve on the candidate's advisory committee. The Examination and Certification Committee then chooses two additional faculty members for that committee and designates a chairman (not the major professor). The candidate should complete both the written and oral preliminary examinations by the end of the fifth semester of continuous enrollment.
The written preliminary examination is a "take-home" examination consisting of five questions written by the five-member advisory committee. The candidate notifies the advisory committee chairman when (s)he is ready to take the examination. The committee chairman then requests questions from the members of the committee and delivers these five questions to the chairman of the Examination and Certification Committee who then provides the questions to the candidate at the start of the examination. The candidate turns in the answers to the chairman of the Examination and Certification Committee within one week after receiving them. (The chairman of the Examination and Certification Committee shall select an alternate from the membership of that committee to handle these tasks in his absence from the University.) The written answers are duplicated in the Biophysics Office and distributed to the student's advisory committee for grading. The results of the examination are communicated within two weeks to the chairman of the Examination and Certification Committee who sends a written summary of the results to the student.
The oral preliminary examination, which is to be taken after successful completion of the written prelim, consists of the defense of a written research proposal. The proposal should describe the background and aims of the candidate's thesis project, important results obtained to date, future research plans, and a timetable for completion of the experiments. It should be on the order of 12 to 18 double-spaced typed pages.
The candidate supplies five copies of this report to the Biophysics coordinator (Pat Omilianowski) who distributes them to the candidate's advisory committee and schedules the oral preliminary examination. (The advisory committee members should have received their copies of the report at least three working days before the scheduled date for the examination.) The Biophysics Office will send the oral prelim rating forms (one for each committee member) to the committee chair prior to the examination.
At the examination, the student first presents an uninterrupted 20-minute survey of the research project with the understanding that the committee members have read the written report. Then each advisory committee member is free to ask the candidate questions pertinent to the research topic and related areas. After the question period, the advisory committee meets in closed session to grade the candidate's performance. An NIH-style rating system is used: scores are recorded on a form in integers from 1 (best) to 5 (worst). An average score of 2.5 is a pass; a score over 2.5 is a fail. The student is called back and told the results of the examination. The chairman of the prelim committee returns the signed rating sheets.
Students are given one opportunity to retake the written or oral part of the preliminary examination in the event of a failed grade.
I. Progress Reports back to top
Candidates who have passed the preliminary examination must prepare a written progress report during the fall semester and supply one copy to each member of their advisory committee and one copy to the Biophysics Office. The report (5-10 pages in length) gives a current summary of research progress, including any difficulties encountered and future plans. It should incorporate pertinent figures and reference citations. It should also list all abstracts, submitted papers, and reprints of articles from the progress period (one copy for each advisory committee member and one copy for the Biophysics Office).
J. Warrants back to top
Candidates who have met course requirements and passed the preliminary examination become eligible for a "preliminary warrant." The Biophysics Office requests the preliminary warrant from the Graduate School. The candidate is responsible for obtaining the signatures of all members of the candidate's advisory committee. The candidate is "certified for the Ph.D." only after the warrant is signed and returned to the Graduate School. At this point the candidate is eligible for "dissertator status."
K. Dissertator Status (Continuous Registration) back to top
Once a candidate has filed the preliminary warrant, (s)he must be registered continuously as a dissertator through the day the Ph.D. thesis is filed with the University Library. For this purpose, registration in a given academic term extends up to the first day of classes of the following term. If a candidate delays in filing the thesis until the first day of classes (or later), (s)he must register for that term. Those who fail to maintain continuous registration are subject to a penalty of 12 times the current per credit fee (dissertator rate).
Dissertators register for 3 credits per academic term (semesters I and II, 8-week summer session) and pay fees at a reduced rate. Generally, the 3 credits include 2 credits of research (990) and 1 credit of advanced seminar in the spring and fall semesters and 3 credits of research (990) in the 8-week summer session.
L. Thesis and Final Exam back to top
Candidates are expected to carry out research during the entire Ph.D. training period. The thesis based on this research must represent "a substantial effort from both the experimental and literary points of view."
The final examination is oral and deals primarily with the candidate's thesis. The final exam committee ordinarily will be the candidate's advisory committee. The committee must include one faculty member who is not in the candidate's major professor's department. The thesis in its final form must be distributed to the members of the final exam committee not less than one week before the date of the final examination. Exceptions to this rule are not granted.
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