Curriculum & Student Handbook The BSCB program administers the Ph.D. in Biophysics. The program provides students with the training to develop into independent scientists capable of doing advanced research in the biophysical and structural biological fields. This program is interdisciplinary and includes faculty mentors in the Department of Biochemistry and Biophysics in the School of Medicine and Dentistry and in the Department of Chemistry in The College of Arts and Sciences. Application to the program is encouraged from students with varied backgrounds including those with previous training in physics, chemistry, biochemistry, biology and computer science. Ph.D. Program Requirements The Ph.D. in Biophysics includes curriculum requirements, attendance and presentation at various seminars, two qualifying examinations, and independent research leading to the thesis. Coursework The curriculum consists of several components: the core course requirements, the general seminar and distribution, and elective courses. The goal is to provide a balanced yet in depth course experience that brings the candidate to the forefront of our current knowledge in one area while elevating general awareness in related fields. In consultation with advisors, the selection of a strong supplementary course program during the first two years in residence is crucial to development of the background necessary to fully participate in the scientific enterprise. We provide some recommendations below that are not in any way intended to be exclusive. Core Curriculum Fall Semester IND 408 – Advanced Biochemistry (5.0 credits) IND 409 – Cell Biology (4.0 credits) IND 501 – Ethics & Prof Integrity in Research (1.0 credit) BPH 571 – Biophysics Seminar (1.0 credit) BPH 592 – Special topics (variable credits) BPH 595 – Phd Research (variable credits) Spring Semester IND 410 – Molecular Biology & Genetics (4.0 credits) BPH 411 – Methods In Structual Biology (5.0 credits) BPH 509 – Molecular Biophysics (5.0 credits) BPH 572 – Seminar In Biophysics (1.0 credit) BPH 595 – Phd Research (variable credits) Elective Courses Any graduate course offered by the University of Rochester may be used as an elective provided it is appropriate to your program and is approved by your advising committee. Some courses that commonly provide needed background for biophysics students are listed below; however, this list is by no means exhaustive. Suggested Electives Fall Semester BIO 402 – Molecular Biology (4.0 credits) BPH 402 – Math Methods of Pso & Med (3.0 credits) BPH 403 – Math for Molecular Bph (3.0 credits) BPH 408 – Math Methods of Bph (4.0 credits) CHM 437 – Syn Design:Strategy&Tactics (2.0 credits) CHM 470 – Computational Chemistry (4.0 credits) MBI 473 – Immunology (3.0 credits) NSC 512 – Cellular Neuroscience (5.0 credits) PHP 403 – Human Cell Physiology (4.0 credits) Spring Semester BCH 412 – Adv topics In Bio Macromlcls (5.0 credits) BCH 570 – Chroma & Transcr Highr Eukar (2.0 credits) BME 442 – Microbiomechanics (2.0 credits) CHM 414 – Biological Inorganic Chemistry (4.0 credits) CHM 422 – Organometallic Chemistry (2.0 credits) CHM 451 – Quantum Chemistry I (4.0 credits) BPH 542 – Special Topics in Cellular Biophysics (2.0 credits) BPH 592 – Special topics (variable credits) IND 443 – Eukaryotic Gene Regulation (4.0 credits) IND 447 – Signal Transduction (4.0 credits) Additional Requirements Student Laboratory Rotations All first year students are required to complete three laboratory rotations during the first year. At the beginning of the academic year, faculty members will present short (30 minute) informal lectures to the incoming students describing their research activities. The goals of this series are to acquaint students with ongoing research in the Program and to alert them to opportunities for their laboratory rotations and future Ph.D. research. At the end of this series of presentations, students sign up for laboratory rotations by submitting a list of their choices to the Graduate Education Committee. The first rotation will be in the Biophysics, Structural and Computational Biology program. Subsequent rotations may bedone in the laboratory of a dissertation advisor from any program, with the advice of the student's advisor. Every effort will be made to accommodate the students' wishes. Students are expected to complete 3 projects in laboratories representing more than one area of interest before requesting assignment to a laboratory in which their Ph.D. research project will be completed. Teaching Assistantship Each student is required to act as a teaching assistant for one semester. Usually, this will be during the second year. However, for those students for whom English is a second language, the teaching assistantship can be delayed until the third or fourth year. Students are welcome to request specific teaching assignments and every effort will be made to accommodate such requests. Assignments are made by the Graduate Studies Director. Student Research Seminars Experience in organizing research data, interpretation of data, synthesis of information from diverse sources, and presentation to an audience of scientific colleagues represents valuable preparation for a career in science whether in an academic or industrial setting. Therefore, students are required to present a yearly seminar in the student series beginning in their second year of studies. During the course of studies students are required to make at least 6 seminar and/or poster presentations. Presentation at the Student Seminar Series or in another approved seminar course will fulfill this requirement. Presentation at a University poster day and presentations made at scientific meetings outside the University may also be used to fulfill the requirement. First Year Preliminary Examination and Evaluation On Monday following exam week in May, each student will be given copies of a dozen or more research articles. The student will select one of the articles and submit a paper which contains three sections: Questions raised by the article Critical appraisal of the article Proposal for additional research Following submission of the document, the student will have an oral examination before a committee consisting of three members chosen by the Graduate Advisory Committee. The oral examination starts with a 20-minute presentation by the student, during which the student presents and explains the results of the study of the selected article. The balance of the examination is devoted to questions raised by the committee. The examining committee assesses the student's performance with respect to four criteria: The student's ability to evaluate published research critically and fairly The student's ability to draw upon formal graduate course work to analyze the research The student's creativity in suggesting new and justified research, to improve and/or extend the study The strength of the content and style of the written document, and the ability of the student to defend, modify or extend the document during oral debate Qualifying Examination The purpose of the Qualifying Examination is to determine whether the student is qualified and competent to continue work toward a Ph.D. in Biochemistry or Biophysics. It is not intended as a test of the proposed research problem or of the supporting experimental data, but rather as a means of determining the potential of the student for independent thought and his or her comprehension of the general field and perspective for exploiting a relevant problem in a scientifically sound manner. The examining procedure involves preparation by the student of a written Ph.D. thesis research proposal. Because a career in science will undoubtedly involve submission and defense of research projects (whether in an academic or industrial setting) we recommend using a modified NIH proposal outline. The Qualifying Examination must be taken before the end of the first semester of the third year. The Qualifying Examination will be carried out by the thesis advisory committee and a member of the Graduate Advisory Committee. The advisor will not be present at the examination. Students must have completed a minimum of 24 hours of course work credit, as outlined above, at the time of the Qualifying Exam. The completed Ph.D. thesis research proposal must be submitted to each member of the thesis advisory committee and to the Department Office at least two weeks before the day of the examination. Exemptions from Requirements All entering students concerned with exemptions from core courses may request an exemption interview to determine whether an exemption is appropriate. The exemption interview will consist of a brief (30-60 minutes) discussion with the course director who will ask questions based on the content of the course to be exempted. The director will then advise the student and the Director of Graduate Studies whether the course needs to be taken. M.D./Ph.D. Program M.D./Ph.D. program students usually enter the Ph.D. portion of their combined degree work after the basic science years of the M.D. curriculum. During the second year of the M.D. program they should discuss the Ph.D. Program in Biophysics with the faculty to plan optimally for the Ph.D. work. Required course work for M.D./Ph.D. students will be arranged between the student, the advisor and the Graduate Studies Director of the Program, taking into account previous training. The teaching assistant requirement is also waived for M.D./Ph.D. students.