Described below are requirements for coursework and teaching assistantships, and expectations for thesis research. In the spring of the second year, graduate students must also pass a Graduate Board Oral exam, a requirement for all graduate students at Johns Hopkins for continuing in their PhD studies.
Students are required to take four core courses during the first year. These courses provide a foundation in molecular biophysics, with emphasis on thermodynamics, molecular structure, and biophysical techniques. Students also need to take at least one elective course, which they will choose in consultation with the course director, based on their proposed thesis research. The four required courses are the following:
AS.250.649 – Introduction to Computation in Biology
This is an intensive “bootcamp”-style course that meets daily for the first few weeks of the fall semester. The course introduces students to the UNIX environment, Python programming, and Mathematica. No prior programming experience is necessary. This course is coordinated with other biophysics classes, helping to reinforce concepts and give students practical experience in using computation for data analysis.
AS.250.689 – Physical Chemistry of Biological Macromolecules
This course intensively delves into the principles of thermodynamics and kinetics of biological molecules. Students will study the theory underlying classical, chemical, and statistical thermodynamics, kinetics, theory of ligand binding, and conformational equilibria. Students are challenged with weekly problem sets, as well as mid-term and final exams.
AS.250.690 – Methods in Biophysics
Students are introduced to seven core methods in biophysics, with lectures on theory accompanied by hands-on experience. Topics include X-ray crystallography, NMR, fluorescence and solution biophysics, single-molecule techniques, ultracentrifugation, molecular dynamics, and statistical analysis. This course is taught in a modular format and does not follow the normal semester-pattern of classes, with each section taught over several consecutive days. In addition to providing a broad overview of current techniques, the practical and theoretical knowledge should help students more quickly dive into research for thesis projects.
AS.250.685 – Proteins and Nucleic Acids
This class uses papers from the scientific literature to introduce students to core concepts of macromolecular structure and energetics. Students are expected to participate in class discussions on each topic, based on assigned readings. Weekly problem sets and two take-home exams reinforce course material. Problems additionally require python scripting, which adds experience in structural analysis via programming. By the end of the course, students should have a strong foundation in the structure and function of proteins and nucleic acids, as well as confidence reading and interpreting the primary literature.
Teaching is an important mission of the Department of Biophysics. Students in the Jenkins Biophysics Program are required to serve as teaching assistants (TAs) for four semesters, which lasts the first two years. As part of their own education and professional training, PhD students provide essential help in running laboratory and computer-based undergraduate courses.
Students can carry out their dissertation research with any tenured or tenure-track faculty member in the Department of Biophysics. The faculty work on a wide range of scientific topics and utilize a range of techniques. To help determine which research group provides the best fit, students take part in two seven-week “rotations” in the Spring semester of the first year. In each rotation, students work with the faculty member of their choice, and thus get exposure to the scientific questions and techniques carried out in each group. A third rotation can also be carried out in the summer before the beginning of the second academic year. In addition to choosing a group for thesis research, we view rotations as learning experiences that should be taken as seriously as required coursework.
Science requires an ability to clearly communicate research findings to the community. To help develop skills in presenting scientific work and ideas to others, students are required to give a 25-minute seminar on their proposed research project during their third year. While we encourage students to include their own data as part of background or preliminary results, it is also acceptable to focus on previous work of others. This experience is meant to both provide an experience in public speaking and help stimulate development of research directions.
In addition to classes, students are required to attend seminars given by outside speakers invited by the Biophysics Department, given on a weekly basis. Meeting and hearing about the work of others provides an excellent opportunity to observe different styles of communicating science, learn about career paths of others, and of course find out what key scientific questions are being pursued in different fields.
Approval for Dissertation Research
After being admitted to the program, students must pass a Graduate Board Oral (GBO) exam to continue their dissertation research at Johns Hopkins University. This exam is traditionally taken in the spring of the second year. The exam committee consists of five faculty members, and the student provides oral answers. While generally focused on biophysics, questions can also extend to topics in biology, chemistry, and physics. Students who feel they may lack a strong background in certain areas are encouraged to improve their knowledge by taking elective classes and self-study during the first two years.
Read more about graduate studies and university policies at Johns Hopkins on the academic catalog website.