Courses Two courses, QCB 515 (Method and Logic in Quantitative Biology) and PHY562 (Biophysics), are required for all BPY 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. Elective Courses 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 MAT586/APC511/MOL511/QCB513ComputationalMethodsinCryo-ElectronMicroscopy MOL 504 Cellular Biochemistry MOL 506 Cell Biology and Development MOL 514 Molecular Biology 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 505 Quantum Mechanics PHY 506 Advanced Quantum Mechanics PHY 509 Quantum Field Theory PHY 511 Statistical Mechanics PHY 525 Introduction to Condensed Matter Physics PHY 535 Phase Transitions and the Renormalization Group QCB 505/PHY555 Topics in Biophysics and Quantitative Biology QCB 508 Foundations of Statistical Genomics 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. 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. Seminars and presentations 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. Committee Meetings 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.