Introduction to Program and Program Rationale
The primary objective of the Biophysics Program at Harvard University is to prepare investigators with diverse backgrounds for independent research careers in which the concepts and methods of physical science are applied to biological problems. The program is administered by the Committee on Higher Degrees in Biophysics, which is comprised of senior representatives from the Departments of Biological Chemistry and Molecular Pharmacology; Molecular and Cellular Biology; Chemistry and Chemical Biology; Physics; Genetics and Pathology. Owing to the interdepartmental nature of the program, research may be pursued on the Cambridge campus (in the Departments of Molecular and Cellular Biology; Chemistry and Chemical Biology; Physics; the School of Engineering and Applied Sciences; etc.) or the Boston campus (including the Harvard Medical School, Division of Medical Sciences, and the 11 Harvard-affiliated teaching hospitals, which include the Dana-Farber Cancer Institute, Children’s Hospital, Massachusetts General Hospital, and the Beth Israel Deaconess Hospital).
The goal of the biophysics program is to nurture independent, creative scientists. To this end, the first part of the program seeks both to introduce the student to the faculty members and their research directly, enabling the student to make a considered choice of research advisor, and to involve the student in the diverse areas of biophysics through laboratory as well as coursework. This first two years provides a background for the second part of the program: the training of the student to be an independent scientist by a period of intensive research, culminating in publications and the PhD degree.
Admissions and Scholarships
Application forms for admission and financial aid may be requested from the Admissions Office, Harvard Graduate School of Arts and Sciences, Holyoke Center, 3rd floor, 1350 Massachusetts Avenue, Cambridge, MA 02138. We encourage online submission of the application. See the website.
Applicants should state clearly in this application their desire to enter the program for the PhD degree in biophysics. All prospective students are urged to file the application forms well in advance of the deadline of December 3. Late applications will not be considered. Scores on the general Graduate Record Examination (GRE) are required except in special circumstances. GRE subject tests are recommended. Due to the early application deadline, applicants should plan to take GRE tests no later than October to ensure that original scores are received by the December 1 deadline. TOEFL is required of all foreign applicants other than those whose native language is English.
Final decisions concerning admission are made by the dean of the Graduate School of Arts and Sciences and the candidates are notified by letter from the Admissions Office.
After being accepted for admission, applicants are encouraged to make arrangements with the administrator of the Committee on Higher Degrees in Biophysics, Building C2, Room 122, 240 Longwood Avenue, Boston, MA 02115, (617-495-3360) to visit the University.
Students with the MD Degree
Students who already have the MD degree will find an opportunity to improve their knowledge of basic science in either of two ways:
1. Opportunities may be available in the several departments to engage in investigations as a research fellow under the direction of a member of the faculty. No university credit toward a degree is given for such work. Questions concerning the appointment of research fellows should be directed to the faculty members.
2. Under special circumstances, students who have received the MD degree may become candidates for the PhD degree in biophysics, providing their qualifications for admission are approved and providing they are prepared to fulfill the normal requirements for the degree.
Combined MD-PhD Program
Students admitted to Harvard Medical School, as candidates for the MD degree, may also apply for admission to the biophysics program in order to earn a PhD degree in biophysics. This program may be of particular interest to prospective medical students with a strong background in physics and to students enrolled in the Harvard-MIT Division of Health Sciences and Technology.
Suggested Undergraduate Preparation
The large list of courses below would provide an ideal background for a student’s coursework in specialized areas of biophysics. No undergraduate major would have taken all these courses in college. Harvard course numbers are provided for further reference.
Introduction to Calculus and Calculus, Series & Differential Equations (Math 1a and Math 1b)
Multivariable Calculus and Linear Algebra and Differential Equations (Math 21a and 21b)
Complex Function Theory (Math 113)
Data Structures and Algorithms (Computer Science 124)
Introductory Mechanics and Relativity (Physics 15a)
Introductory Electromagnetism (Physics 15b)
Wave Phenomena (Physics 15c)
Quantum Mechanics I and II (Physics 143a and 143b)
Introduction to Biophysics (Physics 140)
Organic Chemistry (Chem 20 and Chem 30)
Physical Chemistry and Statistical Thermodynamics (Chem 160 and 161)
Principles of Organic Chemistry (Chem 17)
Evolutionary Biology (OEB 53)
Cell Biology (MCB 54)
Biochemistry and Physical Properties of Macromolecules (MCB 56)
Neurobiology of Behavior (MCB 80)
Molecular Biology (MCB 52)
An Integrated Introduction to the LifeSciences: Genetics, Genomics, and Evolution( Life Sciences 1a)
Advice to International Students
Students from non-US countries who are continuing their studies at Harvard, or who are applying for admission to the University, should communicate with the Harvard International Office, 1350 Massachusetts Avenue, Room 851, Cambridge, MA 02138, which is especially designed to help and advise international students. The immigration and naturalization laws specify many complex legal requirements affecting the status of international students and scholars during their period of study in the United States. The office is prepared to furnish information to aliens on visa requirements, permissible employment, income tax liabilities, and many other official restrictions in effect under existing laws of the United States.
All students accepted into the program are awarded full support, including a stipend, full tuition, and health fees contingent on continued satisfactory progress. Teaching fellowships are available. Second-year students must teach one term as part of their academic requirements. Students are responsible for finding their own teaching position in any one of the participating science departments.
Students are encouraged to apply for external fellowships, such as those administered by the National Science Foundation, the National Defense Science and Engineering Fellowship, and the National Institutes of Health, which are available on a competitive basis to graduate students in biophysics. Applications for those fellowships should be made directly to the appropriate agencies.
Certain limited funds are available as beneficiary aid, distributed by the deans of GSAS to students in the form of gifts or loans to meet unexpected financial needs. Information on loans and beneficiary aids may be obtained from GSAS.
Program of Study
Most graduates of the biophysics program at Harvard have been undergraduate majors in physics or physical chemistry, though a few have come from biology. Consequently, the course requirements for admission are flexible. Each student’s program of graduate study is planned in consultation with a faculty advisor. The degree program is designed to be completed in a maximum of six years.
The first year’s training in the biophysics program provides an introduction to five diverse areas of biophysics: 1) structural molecular biology; 2) cell and membrane biophysics; 3) molecular genetics; 4) physical biochemistry; and 5) neurosciences. The curriculum includes learning experiences in a laboratory environment as well as coursework. The program is flexible and special effort has been devoted to minimizing formal requirements.
The laboratory experience is organized as a full course, Biophysics 300. In the first ten weeks of the fall term, faculty members associated with the biophysics program give seminars describing the current research interests of their own laboratories. Following this, a student spends six-week periods in each of three different laboratories. The list under Participating Faculty and Their Special Fields names some of our professors who currently support biophysics rotation students. In order to make sure that the student gains familiarity with several fields of biophysics, each of the three laboratory experiences usually is selected from a different one of the areas of biophysics listed above. It will also be possible to work on a suitable problem in mathematical biophysics in place of one of the three laboratory rotations.
Biophysics 101, Computational Biology, focuses on modern technologies with exponential growth and their impact on global quality of life through weekly updated Wiki class project (in-depth case studies on personal genomics and/or biofuels). Integrating knowledge, tools for research, and commercial decision-making concerning new aspects of bioengineering, personalized medicine, genetically modified organisms, and stem cells. Interplays of biophysical, ecological, economic, and social/ethical modeling will be explored through multi-disciplinary teams of students, and individual brief reports.
Biophysics 204, Structural Biology From Molecules to Cells, explores imaging of molecules and of molecular localization in cells, including x-ray and electron crystallography, electron microscopy of single molecules, and high-resolution light microscopy.
Biophysics 205, Computational and Functional Genomics, explores experimental functional genomics, computational prediction of gene function, and properties and models of complex biological systems. This course primarily involves critical reading and discussion rather then lectures.
Biophysics 242, Special Topics in Biophysics, invites two or more professors in the spring term to speak on new areas of their own research, thereby introducing students to new questions and methods of research that would not normally be accommodated by the regular curriculum. Past topics have included structure and function of DNA; oncogene products; two-dimensional nuclear magnetic resonance; RNA structure and function; diffusion; atomic interactions in protein-ligand interactions; analysis and design of novel protein-protein and protein-ligand interactions based on 3-D structural information; structure/ function relationships in peptide antibiotics; biological interactions at surfaces; enzyme-catalyzed redox reactions: catalysts and cofactors; molecular neurobiology and systems neurosciences; conceptual foundations and recent developments in computational biology, genomics, and macromolecular interactions; new biology through physics: molecular discoveries with light, information theory and neural systems, X-ray and electron crystallography and high-resolution light microscopy, and computational and functional genomics ; and molecular motors.
In addition to these courses, each student normally takes one course in each of the five biophysics areas mentioned previously. Most coursework is completed within the first two years.
A student may also gain knowledge in a particular area by taking reading courses or by studying independently while registered for TIME.
Courses in Biophysics and
Courses in the following list have been divided roughly into the five areas plus mathematical biophysics. However, the list is not all-inclusive; further offerings for any given term may be found in the Harvard University list of Courses of Instruction.
Structural Molecular Biology
Computational Biology (Biophysics 101)
Chemical Biology (Chemistry 170)
Molecular Biology (BCMP 200)
Proteins: Structure, Function and Catalysis (BCMP 201)
Macromolecular NMR (BCMP 228)
Advanced Organic Synthesis and Reactions (Chemistry 207)
Dynamic and Stochastic Processes in Cells (Systems Biology 200)
Structural Biology of the Flow of Information in the Cell (MCB 156)
Molecular Biology of the Bacterial Cell (Microbiology 201)
Mechanisms of Microbial Pathogenesis (Microbiology 205)
Structural Biology From Molecules to Cells (Biophysics 204)
Molecular Genetics of Neural Development and Behavior (MCB 129)
Computational and Functional Genomics (Biophysics 205)
Bioregulatory Mechanisms (MCB 155)
Principles of Genetics (Genetics 201)
Human Disease (Chemistry 185)
Physical Chemistry (Chemistry 160)
Frontiers in Biophysics (Chemistry 163)
Topics in Biophysics (MCB 212)
Quantum Mechanics for physical Chemistry (Chemistry 242)
Statistical Thermodynamics (Chemistry 161 or Chemistry 240)
Experimental Physical Chemistry (Chemistry 165)
Cell and Membrane Biophysics
Molecular and Cellular Immunology (MCB 169)
Biochemistry of Membranes (MCB 176)
Molecular Biology of the Cell (Cell Biology 201)
Biology of the Cancer Cell (Cell Biology 212)
Molecular and Systems Level Cancer Cell Biology (Cell Biology 211)
Complex and Fourier Analysis (Applied Mathematics 104)
Ordinary and Partial Differential Equations (Applied Mathematics 105)
Methods of Analysis (Math 115)
Physiological Systems Analysis (Eng. Sci. 145)
Nonlinear Dynamical Systems (Applied Mathematics 147)
Statistics for Biology (OEB 153)
Signals and Systems (Eng. Sci. 156)
Physical Mathematics I, II (Applied Mathematics 201, 202)
Mathematical Modeling (Applied Mathematics 115)
Mathematics in Biology (MCB 111)
Cellular Basis of Neuronal Function (MCB 115)
Molecular Neurobiology (MCB 141)
Introduction to Neurobiology (Neurobiology 200)
Neurophysiology of Central Circuits (Neurobiology 204)
Molecular Neurobiology (Neurobiology 221)
Systems Neuroscience (MCB 105)
Formal Academic Requirements
The academic requirement for the PhD degree consists of not less than two years—at least one of which must be in residence at the Harvard Graduate School of Arts and Sciences—devoted to advanced studies approved as suitable preparation for the degree by the Committee on Higher Degrees in Biophysics. In estimating the extent of a candidate’s study for the degree, the advanced work done in other graduate departments of Harvard or of other universities will be considered. A year’s work for a resident student normally consists of four courses (eight half-courses) of advanced grade. Under certain conditions summer courses taken at the Marine Biological Laboratory in Woods Hole may be counted for credit toward the degree.
The biophysics program anticipates completion of formal course studies in the first two years.
Languages. There is no language examination but students are encouraged to gain a reading knowledge of one foreign language, preferably selected from German, Russian, and French.
Dissertation Qualifying Examination. Before beginning dissertation research, it is normally necessary for the student to fulfill the following requirements: (1) pass one Harvard course in each of the six subject areas listed above; (2) do satisfactory work in three laboratory rotations; and (3) submit and defend an original research proposal. The purpose of the oral defense of the qualifying research proposal is to ensure that the student is adequately prepared to embark on dissertation research. The exam is normally taken in the fourth term of residence, before the chair and three examiners knowledgeable in the field of the research proposal. Reexamination will be permitted. As a rule, students will not be permitted to enter the third year of graduate study unless the qualifying examination has been passed.
Dissertation. Selection of a dissertation advisor normally occurs in a student’s second year of study. Independent research on one’s dissertation technically begins once the qualifying examination is successfully completed.
The program policy is that all students who have successfully completed their qualifying exam promptly establish their Dissertation Advisory Committee (DAC). The DAC has several functions. The first will be to approve the student’s dissertation proposal. Second, the DAC, in consultation with the dissertation advisor, will periodically evaluate the progress of the student’s dissertation research. The DAC may make recommendations to the dissertation advisor as well as the student with regard to the student’s progress towards completion of the dissertation. Third, the DAC, in consultation wth the dissertation advisor, will determine at what point the student is ready to defend his or her dissertation.
It is expected that the preparation of a dissertation will usually require full-time for not less than one-and-a-half years after the qualifying examination. The dissertation must give evidence of independent original research and be clearly, logically, and carefully written in good English. The final manuscript must conform to the requirements described in The Form of the PhD Dissertation.
On receipt of the dissertation, the chair of the Committee on Higher Degrees in Biophysics will appoint a reading committee of three to judge the dissertation. The dissertation defense is comprised of two parts: the public seminar and the private defense. In the private defense the candidate will be questioned on the subject of the dissertation and its relation to the student’s special field and collateral subjects. If the reading committee is unable to agree on its recommendations, the question of the acceptance of the dissertation will be decided by the Committee on Higher Degrees in Biophysics.
Upon completion of all the requirements, the original bound dissertation, with the dissertation acceptance certificate signed by the reading committee, and one unbound copy, will be deposited at the Office of the Registrar of the Graduate School, for inspection by any member of the Faculty of Arts and Sciences.
After Commencement, the original bound copy will be deposited in the Harvard Library, open to public inspection. A second bound copy will be kept by the committee chair, and a third bound copy will be kept by the department in which the student worked.
Selected PhD Dissertation Titles
Graham T. Dempsey (2012). “Photoswitchable Fluorescent Probes for Localization-Based Super-Resolution Imaging”
Katherine A. Edmonds (2012). “Structural Studies on the eIF4A-eIF4G Interaction in Translation Initiation”
Charles K. Fisher (2012). “Statistical Characterization of Protein Ensembles”
Elaine Pei-San Gee (2012). “Biophysical and Molecular Determinants in Cell Tension-Mediated Fibronectin Unfolding that Drive Fibrillogenesis”
William Tyler Gibson (2012). “Topological Biases and Feedbacks in Proliferating Tissues”
Robert M. Koffie (2011). “Molecular Imaging of Synaptic Changes in Alzheimer’s Disease”
Andrew M. Leifer (2012). “Optogenetics and Computer Vision for C. elegans Neuroscience and Other Biophysical Applications”
Anna B. Loveland (2012). “Single-Molecule Studies of Eukaryotic DNA Replication”
Jason S. Leith (2012). “The Facilitation of Protein- DNA Search and Recognition by Multiple Modes of Binding”
Benjamin M. Schwartz (2012). “Biometric Navigation with Ultrasound”
Rui Zhen Tan (2012). “Phenomenological Models in Biological Physics: Cell polarity and rDNA
Matthew W. Thomson (2011). “Transcription Factor Dynamics and Cellular Decision