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«BIOPHYSICS PROGRAM & DEPARTMENT OF STRUCTURAL BIOLOGY 2011-2012 STANFORD UNIVERSITY Revised September 2011 Stanford University Stanford University ...»

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Revised September 2011

Stanford University

Stanford University admits students of either sex and any race, color, religion, sexual orientation, or national and ethnic origin

to all the rights, privileges, programs, and activities generally accorded or made available to students at the university. It does not discriminate against students on the basis of sex, race, color, handicap, religion, sexual orientation or national and ethnic origin in the administration of its educational policies, admissions policies, scholarship and loan programs, and athletic and other University-administered programs.

(While every effort is made to ensure the accuracy of the information available at the time copy is prepared for this guide, the Program does not guarantee its accuracy, and reserves the right to make changes at any time without notice.)


Welcome to the Biophysics Program at Stanford. As you know by now, the Biophysics Program is an IDP (Interdisciplinary Program) that is not centralized in a single physical location. Thus, you are one of 30+ Biophysics graduate students who are spread over numerous research laboratories on both sides of Campus Drive.

GOALS This guide is intended to provide you with critical information about the Biophysics Program and about the requirements for the Ph.D. degree. PLEASE READ IT CAREFULLY AND ABSORB IT THOROUGHLY. If you have any questions, please consult the Program Administrator, Kathleen Guan. She will refer you to the Program Director if necessary.


Executive Committee on Biophysics Pande, Vijay Chemistry Director William Weis Structural Biology Executive committee Doniach, Sebastian Applied Physics Executive Committee KC Huang Bioengineering Executive Committee Staff Vijay Pande, Director Clark Center, Room S295 Stanford, CA 94305-5080 Phone: (650) 723--3660 Fax: (650) 725-0259 E-Mail: pande@stanford.edu 2 Kathleen Guan, Pro

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Offices The Biophysics Program office is located in the Fairchild Building, Room D118. This office is run by Kathleen Guan, Administrative Assistant to the Director. Kathleen is the person to see for all administrative questions and problems.

Enrollment Approximately 30+ graduate students are enrolled in the Program at any given time (comprised of prospective Ph.D students and prospective M.D./Ph.D students).

Current Trainee Directory Since our interdisciplinary approach leads to a scattering of students across campus, meeting your fellow students outside of Biophysics 250 may be difficult. To help, we have included a directory of currently-enrolled students and their office/lab addresses and telephone numbers beginning on the next page.

*First year students have mailboxes in the hall way of the Structural Biology Department (Fairchild Bldg. D-100) until they join a permanent research group.

NOTE: Within the University, all telephone numbers begin with the prefix "723", "725", “497”or "498" may be dialed using only the "3", "5", “7”or "8" and the extension number shown in the Directory.


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Before registering for courses, all new students should consult with the Program Director/Advisor (Prof. Vijay Pande for Biophysics; Prof. Ted Jardezky for Structural Biology) in order to plan a program for the first quarter and subsequent quarters until a permanent Faculty Advisor is decided upon. After one quarter of enrollment, you may petition for transfer of credits for any courses that you have completed elsewhere that may substitute for courses in the Program. Please pick up nd "Application for Graduate Residency Credit" at the Student Services Center (Tresidder 2 floor). No more than 45 units can be transferred.

Registration at Stanford University is an internet e-mail-oriented system. Stanford University assumes that all active students will return the following quarter and an "Intent to Enroll" form is now only required for financial aid purpose for the Autumn and Winter quarters. Details are also explained in the University Time Schedule. Copies of the University Time Schedule and the Stanford Bulletin (course guide) are available several weeks before the end of the preceding quarter at the Information Window of the Registrar's Office.


You will receive a University bill in the mail after registering through Axess. Tuition credits for any support you have been awarded are entered on this bill. Please refer to the brochure "The University Bill" you were mailed out this Summer for practical details on how to read and pay your bill. Be proactive about your bill balance as you would be subject to all applicable late fees. Holds could be put on your account preventing you from registering or using your library card. As you soon as you notice a hold or due amount, please contact the Student Financial Services at 3-2181.

If for some reason your University bill does not show credit for your student aid (stipend and tuition) by the deadline, check with the Program office as to the status of your support (most likely it will be a problem with your on-line record not interfacing with the Student Financial Services' billing system in time, but you should check, just in case). ASSU and housing fees are not covered by student aid funds and will be automatically deducted from your quarterly stipend checks. If you do not wish to have these fees automatically deducted, it is your responsibility to make these arrangements with the Student Financial Services. Remember, no two people have identical fees, so there is no universal template to follow. Timely registration will be required each quarter to qualify for health insurance subsidy for yourself and dependents.

5Program Required Research and Section Numbers

As a first-year Biophysics student, you will be paid by the program (unless you have obtained a fellowship) and should register for 10 units each quarter, as ALL the Biophysics students should register for 10 units (the University system has automatically set you up as a full-time student, so please be sure to make this adjustment via AXESS) the University's on-line system for student access to register, add/drop courses, apply for housing, update address, review grades and degree requirement status, request transcripts, etc. before, so you don't receive a bill for outstanding tuition. You must enroll in, and attend, the Biophysics 250 Seminar for Fall quarter. Beginning Fall quarter, you need to enroll in research course Biophysics 300 (Prof. Vijay Pande’ section during your rotation in your first year). As soon as you have selected a "permanent" faculty advisor, you should enroll in Biophysics 300 (your adviser’s section), or at any time you change your faculty advisor, please update your faculty section appropriately. If your advisor does not appear on the course list in Axess, you should call Kathleen at 3-7576. Please send Kathleen an email regarding which groups you are rotating in your first year and when you settle in a group.


Students being supported on the Program's NIH Training Grant MUST be enrolled for 10 units until they qualify for TGR/TMR (Terminal Graduate Registration /Terminal Medical Registration), for each quarter in which a stipend is paid.

Students enrolling for 8-10 units (less than the full-time tuition rate) must make certain that their tuition assessment has been adjusted to reflect this status. To check status or to make this adjustment, use the




Terminal Graduate Registration (TGR) and Terminal Medical Registration (TMR)

TGR/TMR entitles students to all of the usual student benefits. Students in status may register to take courses but must pay the unit tuition rate. Doctoral students are eligible for TGR status when they have been admitted to candidacy, submitted the Doctoral Dissertation Reading Committee form, completed all required coursework and degree requirements other than the University oral exam and dissertation, accrued 135 academic units. Please see Kathleen to obtain this form.

Students should be aware of the first quarter in which they are eligible to become TGR/TM; it is your responsibility to obtain and complete a request for TGR Status form. Be sure to file this request before registration day of the first th quarter of intended TGR status, at the end of your 4 year. TGR students can register TGR directly via AXESS. You need to have already taken 135 units to qualify for TGR status.

Each quarter, a student in TGR/TMR status must enroll in the TGR course 802 in the degree department (Biophysics) for zero units with the appropriate adviser section number. Not enrolling in this course would have consequences on your library and housing privileges. An "N" grade signifies satisfactory progress in a continuing course, and must be received each quarter to maintain registration privileges. An "N-" grade indicates unsatisfactory progress. The first "N-" grade constitutes a warning. The advisor, Program Chair, and student should discuss the deficiencies and the steps necessary to correct them. A second consecutive "N-" grade will result in a hold placed by the Dean of Graduate Studies on future registration. The department is then obligated to review in writing the student's academic status. Future registration will only be permitted when a plan for completion of degree requirements has been reviewed and approved by the department and the Dean of Graduate Studies (Building 1).

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Advisor While your first year academic advisor is Prof. Vijay Pande, and Prof. Ted Jardetzky for SBIO, ultimately, your academic home as a Biophysics Program student will be the laboratory of the faculty advisor with whom you will be pursuing your thesis related research. During the first year, students are encouraged to work in two labs (two rotations), or three if needed, in order to make an informed choice for their thesis research. Based on these rotations, you will select the lab in which you will do your thesis work. The rotation period is a critical part of graduate training, serving to expose every student to a range of possible thesis topics. The choice of an advisor should be done in consultation with the Director; any change of advisor must be approved by the Director 6 The process of choosing an area of research suitable for a Ph.D. in Biophysics and of finding a suitable academic environment in which to pursue this research requires careful thought. Do not feel rushed to accomplish these goals. Some of you may already have very clear ideas about what you propose to work on and under whose guidance. Others of you may be more uncertain about this. The best sources of information are your colleagues and the faculty themselves. Do not hesitate to make appointments with any of the faculty whose research activities you would like to know more about. They will all be delighted to talk with you and many may already have students in the Program.

In the following pages you will find the names, office and phone numbers of faculty in the Program.

Deadlines To be sure that the choice of your thesis lab is made with the benefit of at least two rotations, no formal commitment to enter a lab can be made before April 1 of the first year. During this time please feel free to consult the Director for any help and advice you may require.

As soon as you have identified a research lab where you will be located, please notify the Program office (email Kathleen your lab location and its mail code at kguan@stanford.edu). Until such time, please supply the Program office with your home address, telephone number and e-mail address.

Departmental Relationships

The degree to which a student's day-to-day needs are met in the particular Department in which your research advisor has his/her primary academic appointment varies with the student and the department. In general, all Departments provide mailboxes or some other mechanism for delivery of your mail (during your first year of rotation, we’ll arrange a mailbox for you in Fairchild Building). However, you should remember that while your fellow lab members and other students in the Department in which you do your research may well become your most immediate and significant peer group, that Department has limited responsibility for any of the administrative details that must constantly be transacted to retain your registration, ensure that you are paid your stipend, etc. If you have administrative problems, please email Kathleen.

Faculty Directory Russ Altman Associate Professor of Medicine (Medical Informatics) russ.altman@stanford.edu 5-3394 Mail Code: 5479 MSOB X-215 http://smi-web.stanford.edu/people/altman/ Annelise Barron Associate Professor of Bioengineering aebarron@stanford.edu 1-1151 Mail Code: 5444 Clark Center W300B Steven Block Professor of Applied Physics and of Biological Sciences sblock@stanford.edu 4-4046 Mail Code: 5020 Herrin Lab 029 http://www.stanford.edu/group/blocklab/ 7 Steven Boxer Professor of Chemistry sboxer@stanford.edu 3-4482, 3-4817 Fax Mail Code: 5080 Keck 325 http://www.stanford.edu/group/boxer/ Axel Brunger Professor of Mol. and Cellular Physiology, Neurology and Neurological Sciences,Synchrotron Radiation Lab.

axel.brunger@stanford.edu 650-736-1031, 650-745-1463 Fax Mail Code: 5432 Clark Center E300 http://atb.slac.stanford.edu/ Zev Bryant Assistant Professor of Bioengineering, and by courtesy, of Struct. Bio zevry@stanford.edu 650-724-3090 Mail Code: 5444 Clark Center E302 Manish Butte Assistant Professor of Pediatrics mjbutte@stanford.edu 650-206-2990, 650-721-1324 300 Pasteur Dr.

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