Preparing scientists to reveal the intricacies of living systems through the application of physics and chemistry
Curriculum
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Requirements
Year one requirements
| Term | Required courses | Other requirements |
|---|---|---|
| Late summer |
Onboarding Intensive
|
|
|
Fall term |
Required:
|
Complete First Rotation QBC Journal Club Research in Progress Talks Pizza Talks BBC Seminars State of the Field Lectures |
|
Winter term |
Required:
Option to add an elective of choosing:
|
Complete Second Rotation QBC Journal Club Research in Progress Talks Pizza Talks BBC Seminars |
|
Spring term |
3 mini courses |
Complete third Rotation QBC Journal Club Research in Progress Talks BBC Seminars |
Year one notes
- Onboarding Intensive: One-week immersion that provides basic competency and breadth before the start of the formal curriculum. Fosters group cohesion while breaking down barriers of scientific communication and provides a level playing field.
- State of the Field Lectures: Presentation and discussion with faculty to ask unanswered questions in their field.
- Rotations: 3 ten-week rotations starting Fall quarter. Must include at least 1 experimental and 1 computational. The ability to have an on-campus rotation this year will be made by a case by case basis. Details & Resources: Rotations and Advisor Selection, Conducting Successful Virtual Rotations
- Pizza Talks: Informal faculty presentations of lab research and culture, held weekly.
- Mini courses: Two-week elective courses in Spring that allow for diversification of curriculum. Each student will take 3 mini courses in spring quarter. One of them must be outside Biophysics.
- Fundamentals: Two to three-week elective courses in Fall that allow for diversification of curriculum.
- Advising: Rotations and coursework must be approved by your assigned academic advisor.
Additional year one requirements
| Course | Course information | Description |
|---|---|---|
|
Lab rotations |
BP 215 Fall/Winter/Spring 3 units each, 3 rotations |
3 ten - week rotations (one per quarter), at least 1 experimental, 1 computational Details & Resources: Rotations and Advisor Selection, Conducting Successful Virtual Rotations |
| Biophysics Research in Progress Talks |
BP 223 Fall/winter/spring 1 unit |
This seminar provides graduate students with a forum in which to develop seminar and poster presentation skills, critically organize and critically review scientific data, and analyze and question oral scientific presentations. Students are required to coach with two faculty members who will help them prepare for and evaluate the presentation. |
|
QBC Journal Club |
BP 224 Fall/winter/spring 1 unit |
Journal club presentations by first- and second-year students in BMI, BP, CCB, and PSPG graduate programs. Details: QBC Journal Club Requirements. |
|
Graduate research opportunities |
BP 225 Fall/winter |
Faculty-student talks |
Additional requirements for the duration of your time in the program
| Course | Course information | Description |
|---|---|---|
|
Research Seminars |
BP 220 Fall/winter/spring 1 unit |
Research seminars presented by visiting scientists |
| QBC Retreat | NA | All students are required to attend the annual QBC Retreat. |
Year two requirements
| Course | Course information | Description |
|---|---|---|
|
Must complete by end of second year |
(If selecting an emphasis in Complex Biological Systems, this must be declared at time of qualifying exam) | |
|
Research (every quarter, year two and forward) |
BP 250 Fall/winter/spring 1-8 units |
Research in your thesis lab; sign up every quarter in years two to six |
|
Teaching Assistantship |
Fall, Winter, or Spring |
One quarter teaching assistant position |
|
Biophysics Research in Progress Talks (every quarter offered) |
BP 223 Fall/winter/spring 1 unit |
This seminar provides graduate students with a forum in which to develop seminar and poster presentation skills, critically organize and critically review scientific data, and analyze and question oral scientific presentations. Students are required to coach with two faculty members who will help them prepare for and evaluate the presentation. |
|
QBC Journal Club |
BP 224 Fall/winter/spring 1 unit |
Journal club presentations by first- and second-year students in the BMI, BP, CCB, and PSPG programs Details: QBC Journal Club Requirements |
| Grant Writing |
BP 297 Fall 1 unit |
Support for fellowship applications |
| QBC Retreat | NA | All students are required to attend the annual QBC Retreat |
Year three requirements and beyond
| Course | Course information | Description |
|---|---|---|
|
Advancement to candidacy |
Within 6 months following qualifying examination |
|
|
Annual thesis meetings, year three and forward |
On or around the anniversary of your qualifying examination |
Thesis meetings are to be held at least once per year following completion of oral examination |
|
Ethical Conduct of Science Refresher in Year 5 |
Fall/Winter | Ethical Conduct of Science must be taken once every 4 years |
| QBC Retreat | NA | All students are required to attend the annual QBC Retreat |
Details: Advancement to candidacy and thesis progression.
Sometime in either the fourth or fifth year all students give a talk on their research at the Biophysics program retreat.
Students are expected to graduate within six years of starting the program. Details: Six-year policy. In order to graduate you must submit your thesis to the Graduate Division and give a thesis seminar. Extending time in the program beyond six years is subject to the approval of the Biophysics Executive Committee.
Courses and course materials
Listed below are course requirements and suggestions to optional helpful coursework for the Biophysics Graduate Program, including course name and number, quarters offered, units, and instructors.
Required core courses
BP 204 A and B: Macromolecular Structure and Interactions
Fall/Winter
4 units each
Robert Stroud and Andrej Sali in Fall; Klim Verba, John Gross, Aashish Manglik in Winter
BP 204A: In this course, we will pursue a qualitative and quantitative understanding of the physical basis of macromolecular function. We will examine: the nature and quantification of the forces that drive macromolecular interactions, both intramolecular (macromolecular folding), and with other proteins and ligands; diffusion of macromolecules; the structural underpinnings of the kinetics and thermodynamics of macromolecular reactions; and the physical basis of important biophysical methods. We will examine the distinctions for macromolecules residing in lipid bilayers. The classwork will be mostly interactive with a weekly lecture that informs in class problem solving and discussion of relevant classic and current literature.
BP 204B: Fluency in multiple biophysical methods is often critical for answering mechanistic questions. To train the next generation of biophysicists at UCSF, we have decided to alter the traditional didactic structure by creating a new 6 week “Macromolecular Methods” class that places data collection at the beginning of the course.
BP 205B: Complex Topics in Biophysics
Winter
4 units
This course will complex topics in Biophysics framed around key questions in the fields of Cellular and Systems Biophysics.
Manglik
BP 219: Special Topics in Biophysics (fundamentals, mini orals, and mini courses)
Winter Mini Oral Qualifying Exam
3 units
Verba
This course will walk students through the process of writing a complete research proposal and culminating with a mini oral qualifying examination. Meetings will be sprinkled throughout the fall quarter and meet regularly in the winter quarter per the instructor's schedule.
Spring
3 units
Staff
UCSF Basic Science Graduate Programs collaborate to offer elective courses that allow for diversification of curriculum.
BP 241: Physical Biology
Fall
5 units
Michael Grabe
This is a course on molecular thermodynamics and statistical mechanics in a biological context. It covers the concepts of entropy, enthalpy, free energy, ligand binding, solvation; the properties of water and the hydrophobic effect; solution electrostatics; adsorption; physical and chemical kinetics; polymer properties; and single-molecule dynamics. Each week of the course consists of two lectures focusing on fundamental principles, and one paper discussion session aiming at connecting these physical principles to problems in biology such as enzyme catalysis, protein folding and phase-transitions, and chromatin compaction.
Elective courses
BMI 203: Biocomputing Algorithms
Winter
3 units
Tony Capra
Introduction to computational issues and methods used in the fields of bioinformatics and computational biology. This course emphasizes the implementation, analysis, and validation of methods. It is about attacking computational problems in biology and not the expert use of existing tools. Areas addressed include analytical thinking, problem decomposition, and algorithm design and implementation. Assignments will focus on the design and implementation of key bioinformatics algorithms.
BMI 206: Statistical Methods for Bioinformatics
Fall
3 units
Katie Pollard
Broad survey of bioinformatics with accompanying assignments. Topics covered include genomics, database searching, family/super-family analysis, structural genomics, complex systems, genetic circuits, and protein-protein interactions.
Other requirements
BP 215: Laboratory Rotations (3 rotations over 3 quarters)
Fall/Winter/Spring (first year only)
2 units each rotation
BP 220: BBC Seminar Series
Fall/Winter/Spring
1 unit each
Selected topics by guest lecturers
BP 223: Scientific Communication Seminar (BP Research in Progress Talks)
Fall/Winter/Spring
1 unit each
Aashish Manglik
BP Research in Progress Seminars, forum in which to develop seminar and poster presentation skills, critically organize and critically review scientific data, and analyze and question oral scientific presentations. Students are required to coach with two faculty members who will help them prepare for and evaluate the presentation.
BP 224: Critical Topics in Biophysics (QBC Journal Club)
Fall/Winter/Spring
1 unit each
Lani Wu
QBC Journal Club, critical review of published scientific papers from scholarly journals, including comprehension, analysis, and evaluation of published scientific data.
Graduate Research Opportunities Seminar (BP/CCB Pizza Talks)
Fall/Winter
This course offers first-year students a series of weekly presentations on research interests of basic science faculty. The purpose is to acquaint new graduate students with research projects and opportunities in faculty laboratories.
State of the Field Lectures
Fall
This course offers students a series of discussions on big questions and unsolved problems in Biophysics. It serves to introduce our first year Biophysics students to the state of the field in key areas of biophysics, by UCSF faculty and students who work on these problems.
BP 297: Special Study (NSF Workshop)
Fall
1 unit
Brian Shoichet
Second-year students meet weekly to hone their grant-writing skills with the objective of submitting a fellowship proposal to the National Science Foundation.
GRAD 202: Race and Racism in Science
Fall first years
1 unit
Aimee Medeiros
This introductory course provides the historical background of systemic racism in scientific research. It explores the relationship between notions of race and science and how scientific research has been informed by and perpetuates anti-Black racism. This course also examines the impact of bias and a lack of diversity in science and ways in which to address these deficiencies. Students will learn the principles of social justice-oriented scientific research and its potential.
GRAD 214: Ethics and the Responsible Conduct of Research
Fall/Winter first year, six sessions
1 unit
Faculty
Sessions cover data management, animals in research, human subjects in research, rules and etiquette of publications, procedures and rules of grants, corporate-academic interactions.
Optional online coursework
The following are suggestions from our students to other resources that can be helpful in this program:
- For statistics: OpenIntro - free online course, free textbook
- Class Central - a list of free online courses
- Udacity - very engaging, about 3 to 5 hours per course
