Biophysics
Interdisciplinary PhD in Structural and Computational Biology and Quantitative Biosciences

Courses

The Biophysics program has flexible course requirements that support the training and education of our interdisciplinary student body. The curriculum consist of:

  • The core curriculum (Biophysical Chemistry and Biophysical Spectroscopy), which provide a foundation of biophysical principles
  • The Biophysics seminar, a literature-based seminar on current Biophysics topics, required for students in their first to third year
  • Six more credit from Advanced Electives, chosen from six different specialty areas depending on the interests of the student
  • An Ethics course in the first year
  • Four additional Seminar courses in advanced topics to be taken after the third year
  • Optional Specialty courses that may be helpful to support the student’s thesis topic

Please find below the details that pertain to each component of our curriculum.

Core Curriculum

The goal of the Core Curriculum is to provide a foundation of biophysical principles and methods to our incoming class.

All students are required to take:

  • Chem 665, Biophysical Chemistry, covering equilibrium thermodynamics, chemical kinetics and transport properties, with emphasis on solution behavior and application to noncovalent interactions of biological macromolecules in solution. Offered every Fall and Spring semesters.
  • Chem 668, Biophysical Spectroscopy (for 3 credits). Focuses on the underlying principles and applications of spectroscopic and microscopy methods employed to solve biological problems at the atomic and molecular level. Currently offered typically every Fall semester (otherwise offered every other year).

Advanced Electives

The Advanced Elective provide an opportunity for our student to develop a foundation in topics that are related to their chosen research area.

Students must take at least 6 credits total of advanced elective courses. All elective courses must be at least 2 credits. That means that students can, for example, take two 3-credit courses, three 2-credit courses, or one 2-credit and one 4-credit course to satisfy this requirement. The following list of courses have all been approved as elective courses by the Biophysics Curriculum and Steering Committee.

Pre-approved Elective Courses

STRUCTURE

Offered in the Fall semester:
Offered in the Spring semester:

SPECTROSCOPY & MICROSCOPY:

Offered in the Fall semester:
Offered in the Spring semester:

MODELING & THEORY

Offered in the Fall semester:
Offered in the Spring semester:

COMPUTATION & BIOINFORMATICS

Offered in the Spring semester:

MOLECULAR BIOLOGY

Offered in the Fall semester:
Offered in the Spring semester:

NEUROSCIENCE

Offered in the Fall semester:

Advanced Elective Course Request Process

The program recognizes that it is important that advanced elective courses are tailored for the specific research topic of each student. Students who are interested in different courses, could petition to have them count as an elective course towards their Biophysics graduate degree. The course needs to be approved by the Biophysics Curriculum Committee.

To request a course approval, please use the Advanced Elective Approval Form. The committee has created a set of guidelines to determine whether or not a course meets the desired rigor to count as an advanced elective. Please read through these guidelines before submitting a course approval request.

CHEM 872 The Biophysics Seminar

The Biophysics program’s seminar requirement aims to foster students’ ability to critically read and evaluate research literature, as well as develop strong research presentation skills.

Chem 872 covers current topics of interest in the field of molecular biophysics. In addition, the course provides an opportunity for developing our community, connecting students and faculty in the program.

1st and 2nd Year Students

The Biophysics seminar, Chemistry 872 – Topics in Biophysics, is required each semester during the first two years in the program.

3rd Year Students

Students are required to take Chemistry 872 – Topics in Biophysics for one additional semester (either Fall or Spring).

Information can be found in the course page.

Research Presentation Requirements

4th Year and Up

Students in their fourth year and beyond are required to do two additional oral research presentations in the context of seminar courses, journal clubs, symposia, and/or conferences chosen freely among the following options (each of the following items counts as one):

One oral research presentation delivered in an official Research Seminar Course at UW-Madison

  • At least 15 minutes duration, focusing on the student’s own doctoral research project
  • Delivered in the context of an official Research Seminar Course of one credit or more, with the PI in attendance
  • The student needs to officially register for the course
  • The course instructor needs to certify that the presentation has occurred

One oral research presentation delivered in the context of the Biophysics Seminar Course Chemistry 872 (after the initial five-semester requirement is completed)

  • At least 15 minutes duration, focusing on the student’s own doctoral research project
  • This student does not need to officially register for the course
  • Students interested in this option should contact the Chemistry 872 instructor at least one week before the first day of the course to schedule the presentation
  • The course instructor must certify that the presentation has taken place

One oral research presentation delivered at a National or International conference

  • At least 15 minutes duration, focusing on the student’s own doctoral research project
  • The PI must certify in writing that the presentation has taken place

One oral research presentation delivered at the yearly Biophysics Colloquium at UW-Madison

  • At least 15 minutes duration, focusing on the student’s own doctoral research project
  • The Program Administrator must certify that the presentation has taken place

One oral research presentation delivered at a UW-Madison Science-based Supergroup

  • At least 15 minutes duration, focusing on the student’s own doctoral research project
  • At least three faculty members must be regular attendees and be in attendance during the student’s oral presentation
  • The Supergroup Organizer must be a Faculty Member and is expected to certify that the presentation has taken place
    1. The three faculty members in attendance are not required to be members of the student’s Graduate Committee.
    2. It is recommended that the student choose a relatively large supergroup to prevent accidental absences of the required number of faculty members

To report each presentation, students need to fill out this Qualtrics survey to report it to the program, indicating which seminar option they are completing. This will trigger an email to the instructor/PI/program administrator in charge, asking them to confirm to the Biophysics office that the presentation was given.

Please contact the Biophysics office if there are questions regarding the completion of the seminar requirement.

Students who started prior to Fall 2025

Current students in the program can opt into the new requirements outlined above or meet the old requirements below (attendance of four graduate seminars after year three).

Starting from their fourth year, students are required to attend four more seminar classes in total before their graduation. These are typically a 900-level one-credit course based on presentation and discussion of a journal article or individual research.

These seminar courses provide continued education in current topics in the chosen research area of each student or opportunities for breadth development for topics outside the students’ research areas.

The Biophysics program’s seminar requirement aims to foster students’ ability to critically read and evaluate research literature, as well as develop strong research presentation skills.

Biochem 729 Responsible Conduct of Research

All students are required to take an ethics course in their first year, typically Biochem 729 in the Fall or Spring semester.

Annual Ethics Refresher

In addition, students are required to take a two-hour ethics refresher seminar every year to until graduation. The refresher typically occurs at the end of the Summer semester, and is led by a Biophysics Trainer on a topic of broad interest.

 

Specialty Courses

Students can take additional courses if they are important for their research work and professional development. Students should consult with their Thesis Advisor and thesis committee members about appropriate specialty courses to take pertaining to individual training goals.

990 Research Credits

These are the courses in which students will be conducting their independent research. First semester students will register for 990 research credits in the department of the Biophysics Program Chair, Alessandro Senes. Once a thesis lab is selected, these credits will be conducted in the Thesis Advisor’s home department.

Credit requirements

The Graduate School requires PhD students to complete a minimum of 51 graduate-level credits in order to obtain a PhD Degree. These 51 credits are fulfilled via the combination of core curriculum, ethics course, seminar, specialty courses and 990 research credits. Please keep in mind that all major course requirements must be completed before a student undergoes their oral preliminary examination.

Grade requirements

The Graduate School requires that the overall grade point average (GPA) of non-research courses be 3.0 (B average) or better. In addition, the Biophysics Program requires a cumulative Biophysics GPA of 3.0 or better in the core, ethics, and specialty courses. Research and seminar course grades are not included in the Biophysics GPA.

Credits are not counted from courses in which a grade of BC or below is obtained for either of the Biophysics core courses. In the event of an unsatisfactory grade, the student must repeat the course and obtain a grade of B or better in order to graduate.

The Biophysics Graduate Degree Program Coordinator will monitor course enrollment and completion. Any deficiencies will be discussed with the Biophysics Steering Committee and could lead to academic probation.