Biophysics Academic Year 2023 – 2024 Jump To: Jump To: General Information Address Carl Icahn Laboratory, Lewis-Sigler Institute for Integrative Genomics Phone 609-258-3930 Website Program in Biophysics Program Offerings: Ph.D. Graduate Program Administrator: Jennifer Giraldi Director of Graduate Studies: Joshua Shaevitz Overview The Program in Biophysics (BPY) is intended to facilitate graduate education at Princeton at the interface of the physical and the life sciences. Administered from Lewis-Sigler Institute, Biophysics is a collaboration in multidisciplinary graduate education among faculty in the Institute and the Departments of Chemistry, Chemical and Biological Engineering, Computer Science, Ecology and Evolutionary Biology, Mechanical Engineering, Molecular Biology, Neuroscience, and Physics. The program encompasses the full range of biophysics research at Princeton: from molecules to animals and cells to ecosystems, including work in both experiment and theory. PROGRAM HIGHLIGHTS An Outstanding Tradition: Chartered in 1746, Princeton University has long been considered among the world’s most outstanding institutions of higher education, with particular strength in mathematics and the physics. Building upon the legacies of greats such as Compton, Feynman, and Einstein, Princeton established the Lewis-Sigler Institute of Integrative Genomics in 1999 to carry this tradition of quantitative science into the realm of biology. Princeton University is also the home to the Center for the Physics Of Biological Function, an NSF Physics Frontier Center focused on experimental and theoretical research in biophysics. World Class Research: Biophysics research at Princeton encompasses work on all scales of life. Intact, functioning biological systems are genuinely complex, and it is hard to do the kinds of reproducible, quantitative experiments that are a hallmark of physics. Inside these systems is such a morass of descriptive details that it raises concerns about the value of studying intact systems and processes. However, this sense of gloom is balanced by the fact that living matter organizes itself to do remarkable things. The biophysics community at Princeton attacks these challenges from all angles, combining cutting edge precision experimental measurements and biological manipulation with fundamental theory and phenomenology to make sense of complex biological phenomena. From the mechanics of molecules to communities of bacteria to the development of tissues to networks of thousands of neurons in the brain, we make progress through collaborative efforts that merge different departments and ways of thinking. World Class Faculty: These research efforts are led by the BPY program’s 35 faculty, who include members of the National Academy of Sciences, Howard Hughes Investigators, and early career faculty who have received major national research awards and prizes. Personalized Education: A hallmark of any Princeton education is personal attention. The BPY program is no exception. Group sizes are generally modest, typically 6 – 16 researchers, and all students have extensive direct contact with their faculty mentors. Many students choose to work at the interface of two different groups, enabling them to build close intellectual relationships with multiple faculty. Stimulating Environment: The physical heart of the BPY program is the Carl Icahn Laboratory, an architectural landmark located adjacent to physics, biology, chemistry, and mathematics on Princeton’s main campus. Students have access to a wealth of resources, both intellectual and tangible, such as world-leading capabilities in microscopy, computation, and fabrication. They also benefit from the friendly atmosphere of the Institute, which includes tea and cookies every afternoon. When not busy doing science, students can partake in an active campus social scene and world class arts and theater events on campus. Apply Application deadline December 1, 11:59 p.m. Eastern Standard Time (This deadline is for applications for enrollment beginning in fall 2024) Program length 5 years Fee $75 GRE General Test - optional/not required; Physics or Biology Subject Test - optional/not required Program Offerings Ph.D. Program Offering: Ph.D. Courses Two courses, QCB 515 and PHY562, are required for all students, as is a Responsible Conduct in Research (RCR) course. Three additional elective courses must be completed and can be chosen from the following list. A minimum of a B average in program courses is necessary for successful completion of the program requirement. Courses not on the approved lists may be taken as electives with approval from the DGS. The full course of study for each student must be reviewed and approved by the DGS. APC 524/MAE 506/AST 506 Software Engineering for Scientific Computing CBE 503 Advanced Thermodynamics CBE 517 Soft Matter Mechanics: Fundamentals Applications CHM 503/CBE 524/MSE 514 Introduction to Statistical Mechanics CHM 515 Biophysical Chemistry I CHM 516 Biophysical Chemistry II CHM 538 Topics in Biological Chemistry CHM 542 Principles of Macromolecular Structure: Protein Folding, Structure, and Design CHM 544 Metals in Biology: From Stardust to DNA COS 511 Theoretical Machine Learning COS 524/COS 424 Fundamentals of Machine Learning EEB 504 Fundamental Concepts in Ecology, Evolution, and Behavior II EEB 507 Recent Research in Population Biology ELE 535 Machine Learning and Pattern Recognition MAE 567/CBE 568 Crowd Control: Understanding and Manipulating Collective Behaviors and Swarm Dynamics MAE 552 Viscous flows and boundary layers MAE 550/MSE 560 Lessons from Biology for Engineering Tiny Devices MAE 566 Biomechanics and Biomaterials: From Cells to Organisms MAT 586/APC 511/MOL 511/QCB 513 Computational Methods in Cryo-Electron Microscopy MOL 504 Cellular Biochemistry MOL 506 Cell Biology and Development MOL 514 Molecular Biology 7 MOL 518 Quantitative Methods in Cell and Molecular Biology MOL 521 Systems Microbiology and Immunology MOL 523 Molecular Basis of Cancer MOL 559 Viruses: Strategy Tactics MOL 567 Electron Microscopy in Structural Biology MOL 575 Light Microscopy and Biological Imaging MSE 504/CHM 560/PHY 512/CBE 520 Monte Carlo and Molecular Dynamics Simulation in Statistical Physics Materials Science NEU 437/537 Computational Neuroscience NEU 501A Cellular and Circuits Neuroscience NEU 501B Neuroscience: From Molecules to Systems to Behavior NEU 502A Systems and Cognitive Neuroscience NEU 502B From Molecules to Systems to Behavior NEU 537 Computational Neuroscience NEU 560 Statistical Modeling and Analysis of Neural Data ORF 524 Statistical Theory and Methods PHY 535 Phase Transitions and the Renormalization Group QCB 505/PHY555 Topics in Biophysics and Quantitative Biology QCB 508 Foundations of Statistical Genomics Additional pre-generals requirements First-year rotations All students are required to complete a minimum of two 10-week research rotations during their first year of graduate study, with a maximum of four, to explore possible research advisers. All rotations must be discussed with and approved by the Director of Graduate Studies in advance. Students are required to meet with the faculty member they are rotating with at the beginning of the rotation to form a working plan. Students are expected to show up routinely to work on their project and to attend all group meetings, and it is recommended that the student meet with the faculty member periodically. At the end of each rotation, the department will obtain feedback from both students and faculty. Satisfactory rotation performance is one condition of reenrollment. Most students will have a thesis advisor by the end of their third rotation. If a student foresees a problem in choosing an advisor, they will meet with the DGS to discuss a course of action. General exam The general examination is usually taken in January of the second year and consists of a 7-page written thesis proposal and a 2-hour oral exam on the proposal. The exam committee will consist of three faculty who are not the student’s advisor, with at least two from the training faculty in Biophysics. Qualifying for the M.A. The Master of Arts (M.A.) degree is normally an incidental degree on the way to full Ph.D. candidacy and is earned after a student successfully passes the general examination. It may also be awarded to students who, for various reasons, leave the Ph.D. program, provided the student has completed all coursework, pre-generals requirements, and the written portion of the general examination. Teaching A student must teach a minimum of one full-time assignment (6 AI hours), or teach two or more part-time assignments for a total of 6 AI hours. Students will typically teach in year 3 or 4 of the program. Post-Generals requirements Research progress is overseen by a thesis committee selected by the student after passing the general exam. The committee consists of the thesis adviser and two additional faculty members. At least one member must be the Biophysics training faculty. The thesis committee must be approved by the DGS. Thesis committee members also typically serve as readers and examiners for the dissertation and FPO. Dissertation and FPO The dissertation and final public oral exam (FPO) are required for all Ph.D. students. All students must write and successfully defend their dissertation according to Graduate School rules and requirements. Seminar Biophysics graduate students are required to attend the weekly biophysics seminar series in each semester they are in residence. Each student is also expected to give a talk or poster presentation each year starting in year 2 in either the LSI or CPBF retreats which typically take place during the fall semester. Faculty Director Joshua W. Shaevitz Associated Faculty Mohamed S. Abou Donia, Molecular Biology Robert H. Austin, Physics Bonnie L. Bassler, Molecular Biology Michael J. Berry, Princeton Neuroscience Inst William Bialek, Physics Clifford P. Brangwynne, Chemical and Biological Eng Carlos D. Brody, Princeton Neuroscience Inst Daniel J. Cohen, Mechanical & Aerospace Eng Sujit S. Datta, Chemical and Biological Eng Zemer Gitai, Molecular Biology Thomas Gregor, Physics Bryan T. Grenfell, Schl of Public & Int'l Affairs Mikko P. Haataja, Mechanical & Aerospace Eng Frederick M. Hughson, Molecular Biology William M. Jacobs, Chemistry John Jimah, Molecular Biology Andrej Kosmrlj, Mechanical & Aerospace Eng Andrew M. Leifer, Physics Naomi E. Leonard, Mechanical & Aerospace Eng Simon A. Levin, Ecology & Evolutionary Biology Mala Murthy, Princeton Neuroscience Inst Celeste M. Nelson, Chemical and Biological Eng Sabine Petry, Molecular Biology Gregory D. Scholes, Chemistry Joshua W. Shaevitz, Physics Stanislav Y. Shvartsman, Molecular Biology Howard A. Stone, Mechanical & Aerospace Eng David W. Tank, Princeton Neuroscience Inst Corina E. Tarnita, Ecology & Evolutionary Biology Jared E. Toettcher, Molecular Biology Salvatore Torquato, Chemistry Samuel S. Wang, Princeton Neuroscience Inst Ned S. Wingreen, Molecular Biology Martin Helmut Wühr, Molecular Biology Haw Yang, Chemistry AJ te Velthuis, Molecular Biology For a full list of faculty members and fellows please visit the department or program website. Permanent Courses Courses listed below are graduate-level courses that have been approved by the program’s faculty as well as the Curriculum Subcommittee of the Faculty Committee on the Graduate School as permanent course offerings. Permanent courses may be offered by the department or program on an ongoing basis, depending on curricular needs, scheduling requirements, and student interest. Not listed below are undergraduate courses and one-time-only graduate courses, which may be found for a specific term through the Registrar’s website. Also not listed are graduate-level independent reading and research courses, which may be approved by the Graduate School for individual students. BPY 590 - Extramural Research Internship in Biophysics A summer term, full-time research internship at a host institution to perform scholarly research directly relevant to a student's thesis work. Research objectives are determined by the student's advisor in consultation with the outside host and BPY Director of Graduate Studies. An initial project proposal, monthly progress reports, and a final report are required.