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Biophysics

Contact

Office: Alway Building, Room M116I
Mail Code:
Phone: (650) 723-7576; (650) 498-8179
Email: biophys-ssa@lists.stanford.edu
Web Site: http://med.stanford.edu/biophysics

Overview

Courses offered by the Biophysics Program are listed under the subject code BIOPHYS on the Stanford Bulletin's ExploreCourses web site.

The Biophysics Program offers instruction and research opportunities leading to the Ph.D. in Biophysics. Students admitted to the program may perform their graduate research in any appropriate department.

The Stanford Biophysics Program is an interdisciplinary, interdepartmental training program leading to the Ph.D. Degree in biophysics. The program centers on understanding biological function in terms of physical and chemical principles. The Program comprises faculty from 16 departments in the Schools of Humanities and Sciences, Medicine, Engineering, and the Stanford Synchrotron Radiation Laboratory. Research in the Program involves two overlapping branches of biophysics: the application of physical and chemical principles and methods to solving biological problems, and the development of new methods.

The Biophysics Program aims to train students in quantitative approaches to biological problems, while also developing their perspective in choosing forefront biological problems. A balanced academic program is tailored to the diverse backgrounds of the students. The program requires graduate-level coursework in physical and biological sciences, participation in seminar series, and most importantly achievement of a high level of proficiency in independent research.

Learning Outcomes (Graduate)

The Ph.D. is conferred upon candidates who have demonstrated substantial scholarship and the ability to conduct independent research and analysis in Biophysics. Through completion of advanced course work and rigorous skills training, the doctoral program prepares students to make original contributions to the knowledge of Biophysics and to interpret and present the results of such research.

Graduate Program in Biophysics

For information on the University's basic requirements for the Ph.D. degree, see the "Graduate Degrees" section of this bulletin.

Admissions

For more information, please refer to the Program Curriculum page.

Course Requirements

For more information, please refer to the Program Curriculum page.

Lab Rotation and Settlement

During the first year of graduate school in Biophysics, students are encouraged to complete a minimum two quarters of rotations in any faculty labs of their choice, a third rotation is allowed if necessary. Once the students finish their rotations, they make an official decision on which faculty’s lab to settle in. If the faculty is not part of Biophysics, then the student needs to have an additional co-advising faculty member on their committee who is in Biophysics. Once the student settles in a lab, s/he is required to complete the first Individual Development Plan (IDP) and begin forming the reading committee.

Individual Development Plan (IDP)

In light of the benefits to trainee development and the likelihood that the IDP program will be a factor in NIH funding decisions, the Committee on Graduate Admissions and Policy (CGAP) has adopted a new policy requiring all Biosciences Ph.D. candidates and their mentors in the Schools of Medicine and H&S to create and discuss the Individual Development Plan (IDP) on an annual basis.

  1. Complete the first IDP meeting with the adviser within 30 days of joining the thesis lab.

  2. IDP meetings are required annually, in addition to and separate from thesis committee meetings (see below).

Reading Committee

See the "Degree-Specific Requirements (Doctoral Degrees)" section of this bulletin for University rules concerning doctoral degrees. See GAP 4.8, for further details on the Doctoral Dissertation Reading Committee.

Once a student have chosen a research adviser and  begun thesis-related research, s/he is required to select a reading committee. The student’s reading committee should be in place no later than Autumn Quarter of the third year in the program. The individuals selected by the student serve as an advising and consultative group for the duration of their graduate studies. They evaluate the student’s dissertation proposal and constitute the core of their the defense committee. Students should consult with their research adviser on the selection of their reading committee.

The doctoral dissertation reading committee consists of the principal dissertation adviser and, typically, two other readers. The doctoral dissertation reading committee must have at least three members and may not have more than five members. All members of the reading committee approve the dissertation. At least one member must be from the student's major department. Normally, all committee members are members of the Stanford University Academic Council or are emeritus Academic Council members.

The reading committee, as proposed by the student and agreed to by the prospective members, is endorsed by the chair of the major department on this Doctoral Dissertation Reading Committee form. The student's department chair may, in some cases, approve the appointment of a reader who is not a current or emeritus member of the Academic Council (via the Petition for Non-Academic Council Doctoral Committee Members form), if that person is particularly well qualified to consult on the dissertation topic and holds a Ph.D. or equivalent foreign degree). All examiners must hold a Ph.D. degree (or foreign equivalent). Former Stanford Academic Council members and non-Academic Council members may thus on occasion serve on a reading committee.

Any member of the Academic Council may serve as the principal dissertation adviser. If former Academic Council members, emeritus Academic Council members, or non-Academic Council members are to serve as the principal dissertation adviser, the appointment of a co-adviser who is currently on the Academic Council is required. This is to ensure representation for the student in the department by someone playing a major adviser role in completion of the dissertation. However, a co-adviser is not required during the first two years following retirement for emeritus Academic Council members who are recalled to active service. If the reading committee has four or five members, at least three members (comprising the majority) must be current or emeritus members of the Academic Council.

Qualifying Exam

Once students enter their third year of graduate studies, they are required to arrange a meeting with their committee to present to them a proposed thesis related research project (dissertation proposal).  The meeting is called the qualifying exam, and should be completed no later than the end of Autumn Quarter of the student’s third year. In anticipation of the exam, the student should prepare an approximately 10-page summary of their proposed research and/or any progress they have made at that time. The precise format (e.g., inclusion of a timeline, methods section, etc.) is flexible, and naturally can conform to the particular style of papers or proposals coming from their thesis lab. The main goal of the written portion is to briefly summarize the student’s progress so far and carefully plan out their future thesis research plans with committee feedback and advice.

At the meeting, the student should be prepared to make a 30-45 minute presentation of their research where they discuss their results to date and propose further experiments. Audiovisual aids are not required, but may be useful if available. After completing the qualifying exam, students need to arrange annual thesis committee meetings with their committee members to review academic progress each year. Completing the qualifying exam serves to meet the student’s first thesis committee meeting requirement. The thesis committee meetings should be completed once a year during the student’s 3rd and 4th years, and twice a year past their fifth year and above.

Candidacy

Admission to candidacy for the doctoral degree is granted by the major department following a student's successful completion of qualifying procedures. Students are expected to be admitted to candidacy by the end of the second year of doctoral study. Candidacy is valid for five years, subject to satisfactory academic progress.

Terminal Graduate Registration (TGR)

Doctoral students who have been admitted to candidacy, completed all required courses and degree requirements other than the University oral exam and dissertation, completed 135 units or 10.5 quarters of residency (if under the old residency policy), and submitted a Doctoral Dissertation Reading Committee form, may request Terminal Graduate Registration (TGR) status to complete their dissertations. Students with more than one active graduate degree program must complete residency units between all active/completed degree programs in order to apply for TGR status. See the "Residency Policy for Graduate Students" section of this bulletin for additional information.

Dissertation/Oral Exam

The student must prepare a dissertation proposal defining the research to be undertaken, including methods of procedure. This proposal should be submitted by Autumn Quarter of the third year, and it must be approved by a committee of at least three members, including the principal research adviser, and at least one member from the Biophysics Program. The candidate must defend the dissertation proposal in an oral examination. The dissertation reading committee normally evolves from the dissertation proposal review committee.
The student must present a Ph.D. dissertation as the result of independent investigation that expresses a contribution to knowledge in the field of biophysics. The student must pass the University oral exam, taken only after the student has substantially completed the dissertation research. The examination is preceded by a public seminar in which the research is presented by the candidate.

COVID-19 Policies

On July 30, the Academic Senate adopted grading policies effective for all undergraduate and graduate programs, excepting the professional Graduate School of Business, School of Law, and the School of Medicine M.D. Program. For a complete list of those and other academic policies relating to the pandemic, see the "COVID-19 and Academic Continuity" section of this bulletin.

The Senate decided that all undergraduate and graduate courses offered for a letter grade must also offer students the option of taking the course for a “credit” or “no credit” grade and recommended that deans, departments, and programs consider adopting local policies to count courses taken for a “credit” or “satisfactory” grade toward the fulfillment of degree-program requirements and/or alter program requirements as appropriate.


Graduate Degree Requirements

Grading

The Program of Biophysics counts all courses taken in academic year 2020-21 with a grade of 'CR' (credit) or 'S' (satisfactory) towards satisfaction of graduate degree requirements that otherwise require a letter grade provided that the instructor affirms that the work was done at a 'B-' or better level.

Faculty

Director of Graduate Studies:

  • KC Huang (Bioengineering)

Emeritus:

  • Philip C. Hanawalt (Biology, Dermatology)

  • Harden M. McConnell (Chemistry)

  • Stephen J. Smith (Molecular & Cellular Physiology)

  • Norbert Pelc (Bioengineering, Radiology)

Professors:

  • Russ Altman (Bioengineering, Genetics, Medicine - Biomedical Informatics)

  • Manuel Amieva (Microbiology & Immunology, Pediatrics)

  • Steve M. Block (Applied Physics, Biology)

  • Steven Boxer (Chemistry)

  • Anne Brunet (Genetics)

  • Axel Brunger (Molecular & Cellular Physiology)

  • Wah Chiu (Bioengineering)

  • Gilbert Chu (Oncology, Biochemistry)

  • Steven Chu (Physics, Molecular & Cellular Physiology)

  • Jennifer Cochran (Bioengineering)

  • Bianxiao Cui (Chemistry)

  • Hongjie Dai (Chemistry)

  • Mark Davis (Microbiology & Immunology)

  • Sebastian Doniach (Physics, Applied Physics)

  • Barbara E. Engelhardt (Biomedical Data Science)

  • James Ferrell (Chemical & Systems Biology, Biochemistry)

  • Daniel Fisher (Applied Physics)

  • Judith Frydman (Biology, Genetics)

  • Chris Garcia (Molecular & Cellular Physiology, Structural Biology)

  • Gary H. Glover (Radiology)

  • Miriam Goodman (Molecular & Cellular Physiology)

  • William Greenleaf (Genetics)

  • Daniel Herschlag (Biochemistry)

  • KC Huang (Bioengineering)

  • Christine Jacobs-Wagner (Biology)

  • Theodore Jardetzky (Structural Biology)

  • Shamit Kachru (Physics)

  • Michael Kapiloff (Ophthalmology)

  • Peter S. Kim (Biochemistry)

  • Brian Kobilka (Molecular & Cellular Physiology)

  • Eric Kool (Chemistry)

  • Ron Kopito (Biology)

  • Roger D. Kornberg (Structural Biology)

  • Craig Levin (Radiology)

  • Michael Levitt (Structural Biology)

  • Richard Lewis (Molecular & Cellular Physiology)

  • Sharon Long (Biology)

  • Crystal Mackall (Pediatrics, Medicine)

  • Todd Martinez (Chemistry)

  • Tobias Meyer (Chemical & Systems Biology)

  • W. E. Moerner (Chemistry)

  • Vijay Pande (Chemistry)

  • Dmitri Petrov (Biology)

  • Joseph D. Puglisi (Structural Biology)

  • Stephen Quake (Bioengineering, Applied Physics)

  • Jianghong Rao (Radiology)

  • Mark Schnitzer (Biology, Applied Physics)

  • Jan Skotheim (Biology)

  • Edward I. Solomon (Chemistry)

  • Andrew Spakowitz (Chemical Engineering)

  • James A. Spudich (Biochemistry)

  • Alice Y. Ting (Genetics)

  • Shreyas Vasanawala (Radiology)

  • Anthony Wagner (Psychology)

  • Soichi Wakatsuki (Photon Science, Structural Biology)

  • Thomas Wandless (Chemical & Systems Biology)

  • William I. Weis (Structural Biology, Molecular & Cellular Physiology)

  • Richard Zare (Chemistry)

Associate Professors:

  • Annelise Barron (Bioengineering)

  • Onn Brandman (Biochemistry)

  • Zev Bryant (Bioengineering)

  • David Camarillo (Bioengineering)

  • Ovijit Chaudhuri (Mechanical Engineering)

  • Jose R. Dinneny (Biology)

  • Lynette Cegelski (Chemistry)

  • Rhiju Das (Biochemistry)

  • Adam de la Zerda (Structural Biology)

  • Ron Dror (Computer Science)

  • Alexander Dunn (Chemical Engineering)

  • Liang Feng (Molecular & Cellular Physiology)

  • Olivier Gevaert (Biomedical Informatics, Biomedical Data Science)

  • Pehr Harbury (Biochemistry)

  • Jin Billy Li (Genetics)

  • Lingyin Li (Biochemistry)

  • Jan Liphardt (Bioengineering)

  • Merritt Maduke (Molecular & Cellular Physiology)

  • Ashby Morrison (Biology)Mo

  • Manu Prakash (Bioengineering)

  • Kristy Red-Horse (Biology)

  • Julia Salzman (Biochemistry)

  • Sindy Tang (Mechanical Engineering)

  • Roseanna Zia (Chemical Engineering)

Assistant Professors:

  • Monther Abu-Remaileh (Chemical Engineering)

  • Raag Airan (Radiology)

  • Christopher O. Barnes (Biology)

  • Lacramioara Bintu (Bioengineering)

  • Alistair Boettiger (Developmental Biology)

  • Gheorghe Chistol (Chemical & Systems Biology)

  • Jonas Cremer (Biology)

  • Laura M.K. Dassama (Chemistry)

  • Shaul Druckmann (Neurobiology, Psychiatry & Behavioral Sciences)

  • Polly Fordyce (Genetics)

  • Xiaojing Gao (Chemical Engineering)

  • Matthias Garten (Bioengineering)

  • Benjamin Good (Applied Physics)

  • Keren Haroush (Neurobiology)

  • Possu Huang (Bioengineering)

  • Anshul Kundaje (Genetics, Computer Science)

  • Jonathan Long (Pathology)

  • Michaelle Ntala Mayalu (Mechanical Engineering)

  • Julia Palacios (Biomedical Data Sciences, Statistics)

  • Johannes Reiter (Radiology, Biomedical Data Science)

  • Grant M. Rotskoff (Chemistry)

  • Manish Saggar (Psychiatry & Behavioral Sciences)

  • Serena Sanulli (Genetics)

  • Naima Sharaf (Biology)

  • Katrin J. Svensson (Pathology)

  • Longzhi Tan (Neurobiology)

  • Hawa Racine Thiam (Bioengineering)

  • Bo Wang (Bioengineering)

  • Brad Zuchero (Neurosurgery)

Courses

Stanford Course Catalog website: https://explorecourses.stanford.edu/