PhD or MA in Physiology & Biophysics

The Department of Physiology & Biophysics at the Boston University School of Medicine offers programs leading to the PhD or MA. Each program stresses laboratory training and original research performed under the direction of a faculty member, as well as satisfactory performance in graduate coursework.

In the first and second years of both the PhD and MA programs, a core curriculum of biophysics and physiology is supplemented with Foundations in Biomedical Sciences courses. The course program emphasizes flexibility and individual choice. In the first year, students do research rotations in the laboratories of three or four faculty members to gain firsthand knowledge of a variety of research areas.

At end of the first year, students select a degree advisor and begin laboratory research towards the PhD degree. In the second year students continue to take courses and PhD students must pass a qualifying exam. Throughout their training, students also participate in a weekly department seminar series and report their research progress annually at a student seminar day.

Purpose and Background

The Department of Physiology & Biophysics, under the aegis of Dr. David Atkinson as chair, brings together 22 active faculty members to provide excellence in research and graduate education. Research interests in the department span the modern areas of cellular physiology and molecular biophysics, with strong concentrations in structural biology, vision research, muscle physiology, and the biology and physical chemistry of proteins, lipids, and lipoproteins. Faculty members are nationally and internationally recognized as leaders in their chosen areas of research. The department provides flexible graduate programs with pathways either leading towards a degree in physiology or in biophysics. The department offers these two programs in a strong, collegial environment to encompass and promote the diverse overlapping research of all members of the department.

The goal of our programs in Physiology & Biophysics is to produce graduate students who understand the thermodynamic, chemical, electrical, and structural aspects of biological systems at the atomic level and in the context of the cell and organism. The training across scientific and medical disciplines provides graduates the advantage of learning physiology and biophysics in the context of the regulation of homeostasis and pathogenicity of the cell, and of the organism as a whole. Graduates will be able to communicate and collaborate effectively with a broad range of disciplines ranging from medical personnel to chemists, engineers, and physicists.

A set of required core courses will be taken by the students in the first and/or second year that will lead to a level of understanding of the two disciplines necessary for a degree in physiology or biophysics. After completing the core course requirements, students have flexibility to choose the appropriate additional coursework for their interests, within the guidelines set out below. The courses for first year students are chosen with the guidance of members of the duly constituted Student Admissions & Affairs Committee (SAAC), and in the second year with input from their PhD or MA advisor. Students who successfully complete the program are awarded either a PhD or an MA in Physiology or in Biophysics.

Similar paths for PhD and MD/PhD students

Requirements for PhD and MD/PhD students are similar. Students in the PhD program take their qualifying examination in their second year. MD/PhD students enter after completing the second year Medical Curriculum and are therefore treated as post-master’s students with a lower course and credit requirement (32 versus 64 total credits), and take their qualifying exam at the end of their first year in the program.

Other students entering into the programs with a master’s degree from within the U.S. are treated similarly and take their qualifying examination at the end of the first year. In both cases, post-master’s students are able to choose a suitable set of courses tailored to their backgrounds and research interests, with input from the SAAC during the first year and from their advisor in following years.

Transfer students are handled on a case-by-case basis, but may be able to take the qualifying examination at the end of their first year.

The MA programs

Master’s programs in Physiology & Biophysics are offered. In some cases, a qualified MA student may proceed into the PhD program. This decision will be handled by the SAAC on a case-by-case basis. An MA requires 32 credit hours (paid for by the student) and requires either a literature-based thesis or a short laboratory-based thesis with two readers from within the department.

The Path of a Graduate Student

Special Topics Seminar course (GMS BY 871, 872: 4 credits spread over 2 semesters)

In the first and second years, all students take the Special Topics Seminar course aimed at developing the student’s ability to read the scientific literature and write grant proposals.

Each student presents the merits and/or deficits of a current research paper in front of other students and a proctoring faculty member. The students use a blackboard and computer projector during their presentations. Typically, all students present at least once each semester, and possibly more often, based on the number of enrolled students.

Didactic lectures are combined with writing assignments that prepare students for writing scientific grant proposals, their written qualifying exam, and scientific papers. This class meets for one-and-a-half hours each week, and is supplemented with attendance at Departmental Seminars, where students broaden their scientific knowledge by being exposed to cutting-edge research by outstanding speakers.
Post-bachelor’s students take three semesters (6 credits), while post-master’s, MD/PhD, MA, Cell & Molecular Biology (CMB), and Neuroscience students who enter into laboratories within the department take two semesters (for a total of 4 credits).

The faculty member who teaches this course is rotated after each semester to allow a fresh viewpoint and area of expertise to be covered. The Chair of the SAAC, with input from the Program Steering Committee, selects 6–8 faculty members who are interested in teaching this course on a rotating basis.

Student Seminars

In years 3–5, or starting with the spring term after the qualifying examination has been completed, all graduate students will present a 20–30 minute seminar on their thesis research. These seminars form a logical extension of the departmental Seminar Series and the Special Topics course and take place on a specified Student Seminar Day (or days) scheduled in April or May. Pre-thesis committee members for a presenting student take notes on the quality of the presentation and meet with the student within 2–3 days, on either a one-to-one basis or in small groups with other committee members, to provide feedback with the goal of improving the student’s presentation skills.

Student Posters Presentations

Students who have completed their qualifying exams present a poster during Russek Day in the spring of each year, to improve their organization and presentation skills. These students also present their posters at the departmental retreat held each fall. In addition, students are encouraged to enter their posters in the Science Day poster competition held at the Boston University Charles River Campus. Students are encouraged to attend local and national meetings to present their research.

Course Requirements

Incoming PhD and MA students are required to take four modules from Foundations in Biomedical Sciences, including Protein Structure, Cell Dynamics, and Cellular Physiology (FC 701, 703, 707; 12 credits total). To allow flexibility for the breadth of the fields of physiology and biophysics, yet ensure a working knowledge of both, students are required to take a minimum of one physiology course and one biophysics course. The acceptable physiology courses are:

  • PH 771 A Foundations of Structural Biology: Structure Determination by Crystallography and Electron Microscopy (2 cr)
  • BY 771 B Foundations of Structural Biology: Computation, Thermodynamics, Spectroscopy, and NMR (2 cr)
  • BY 760 A Macromolecular Assemblies: Protein-Protein, Protein-Nucleic Acid, and Membrane Protein Assemblies (2 cr)
  • BY 760 B Macromolecular Assemblies: Lipid-Protein Assemblies (2 cr)

Elective coursework is chosen jointly by the student and their advisor or thesis committee. To achieve a balanced curriculum for all students, the PhD degree requirements of the Division of Graduate Medical Sciences include a minimum of 24 credits in formal coursework. or 12 credits for the post-master’s. It is expected, although not required, that the formal course work credits are acquired prior to the qualifying examination at the end of the second year. Beyond 32 coursework credits, students are encouraged to informally audit courses following consultation with their thesis committee. Post-master’s students who have already taken an appropriate graduate-level course in the core curriculum are permitted to substitute an elective or electives in the first semester, as long as the total semester course credits remain 10.

A Sample Curriculum

Fall semester, first year—all students

  • FC 701 Protein Structure, Catalysis, and Interaction (2 cr)
  • FC 702 Structure and Function of the Genome (2 cr)
  • FC 703 Architecture & Dynamics of the Cell (2 cr)
  • BY 760 A Foundations in Biophysics and Structural Biology (2 cr) or PH 731 Human Physiology A (4 cr)
  • BY 871 Special Topics Seminar Course (2 cr)

Spring semester, first year

  • FC 704 Mechanism of Cell Communication (2 cr)
  • FC 707 Cellular Physiology
  • BY 760 Foundations in Biophysics and Structural Biology (, 2 cr) orPH 732 Human Physiology B (4 cr)*
  • BY 872 Special Topics Seminar Course (2 cr)

*Students fulfilling their physiology requirement with Human Physiology A and B would fulfill their biophysics requirement in their second year.

Fall semester, second year

  • BY 871, 872 Special topics/student seminar (2 cr)
  • BY 771 A Macromolecular Assemblies (2 cr)
  • Electives

Spring semester, second year

  • BY 872 Special topics/student seminar (2 cr)
  • BY 771 B Structural Biology (2 cr)
  • Electives

Suggested Electives

Department of Physiology & Biophysics

  • PH 542 Human Physiology A (4 cr)
  • PH 543 Human Physiology B (4 cr)
  • BY 760 Foundations in Biophysics and Structural Biology (4 cr)
  • BY 771 Biophysics of Macromolecular Assemblies (4 cr)
  • BY 772 NMR Spectroscopy in Biology and Biochemistry (2 cr)
  • BY 774 Metabolism and Cellular Function of Complex Lipids (2 cr)
  • PH 745, 746 Special Topics (e.g. Biology of Vision, Calcium, and Cell Function) (2 cr)

The Qualifying Examination

Success in science requires that students be able to express their thoughts both verbally and in written form. The necessary verbal skills are developed through participation in the Special Topics seminar course and by giving presentations in yearly research seminars at the Student Seminar Day(s), laboratory group meetings, pre-thesis meetings, and the thesis defense seminar. Written skills are developed in required coursework and in the writing of papers and the thesis. This process begins with writing a research proposal using the NIH National Research Service Award (NRSA) or American Heart Assocation Research Training Grants and Fellowships format, to fulfill the written qualifying exam requirement.

The qualifying examination is given at the end of the second semester within the second year for PhD students. MD/PhD, post-master’s, and some transfer students in the PhD program have the option of taking the qualifying examination at the end of the second semester of the first year. Administration of the qualifying examination will be overseen by the SAAC. Program faculty members serve on the qualifying examination committees on a rotating basis. The two-part exam consists of:

  1. For the written qualifying examination students write a research proposal that correlates with, but may or may not include, his/her planned thesis research. This document is judged by three members of the SAAC committee for the student’s understanding of the relevant scientific literature and ability to propose testable scientific hypotheses.
  2. An oral examination where the student is assigned 3 current research papers to read and is subsequently tested on their understanding of the material in front of an examining committee. This committee is comprised of five program faculty members. Papers are chosen by the committee and given to the students two to three weeks in advance of the oral examination. Thesis advisors will not participate in the oral defense of students who are pursuing a PhD in their laboratory.

Both the written and oral portion of the qualifying exam must be passed in order for a student to continue in the PhD program. Students who fail either the oral or the written portion of the exam (or both) can retake that portion of the exam once in order to achieve a passing score. Master’s students do not take the qualifying examination.

Thesis

Pre-thesis meetings

After the student has passed the qualifying exam, a pre-thesis committee of at least five members must be established in the fall of that year and submitted to the SAAC. Students submit their thesis proposal in grant form to the members of the committee two weeks before the first pre-thesis committee meeting. At least one member from outside the department, and preferably from a different institution, should be included in the final thesis committee. An external committee member is not required for pre-thesis meetings, which will be held about every 10–12 months or at least three times prior to graduation.

Thesis defense

The PhD thesis defense consists of a public seminar followed by a closed door thesis defense with a minimum of five committee members, including one member from outside the department.

Program Resources

All members of the faculty of the Department of Physiology & Biophysics participate in the graduate programs in Physiology & Biophysics. The faculty have well funded research programs and extensively equipped individual laboratories for carrying out research in cellular physiology and biophysics. In addition, the department maintains core facilities in molecular biology, spectroscopy, X-ray crystallography, NMR, and structural electron microscopy that will be used by students carrying out their research.

Admission

Recruitment directly into the Program in Biomedical Sciences is the preferred route of entry for PhD students, and MA candidates apply directly to our programs in Physiology or in Biophysics.

There is no strict formula for acceptance to the programs and many factors go into the Admissions Committee’s decisions. The programs seek students from a wide range of backgrounds including physics, chemistry, biochemistry, biology, and medical sciences.

For acceptance into the program, students should have outstanding grades in a rigorous curriculum and applicants should have completed organic chemistry, physics, and physical chemistry courses. The GRE general test is required and the subject test is recommended. Foreign students are required to take the TOEFL. We are especially interested in candidates with research experience. Finally, the letters from the applicant’s references are extremely important, as is the applicant’s personal statement. Underrepresented minorities are encouraged to apply.

Administration

The Chair of the Department of Physiology & Biophysics is the director of the graduate programs and has the ultimate responsibility for administering the graduate programs in Physiology & Biophysics. A Program Steering Committee oversees the graduate programs and advises the Chair of the Student Admissions & Affairs Committee (SAAC) on specific needs of the programs. Steering Committee members select faculty members to serve on the SAAC and oversee the appointment of committees that deal with developing new courses along with the review and updating of existing courses.

The Steering Committee and the SAAC Chair work jointly to supervise the appointment of faculty to run the departmental seminar series and plan the departmental retreat. Student Seminar Days are organized by faculty members who are running the department seminar series in a given year.

The Student Admissions and Affairs Committee (SAAC)

The SAAC oversees the day-to-day operations of the graduate programs, including: student recruitment, admissions, orientation, rotations, assignment of dissertation advisors and administering the qualifying examinations. The SAAC is comprised of 5–7 faculty members that adequately represent the diverse research interests within the department.

The SAAC serves many roles in the department. The SAAC is charged with overseeing student affairs and academic standing, curriculum development, and administering the qualifying examination. The SAAC is also available to help with student problems and to mediate issues between students and advisors.