Mathematical and Computational Modeling of Lung Development
Jan Christoph, Professor
UC San Francisco
Applications for Fall 2026 are closed for this project.
This project is a joint project between the Christoph and Chuang labs at the Cardiovascular Research Institute at UCSF. The Christoph lab studies the heart and cardiac physiology using computational modeling and 3D imaging. The Chuang lab studies lung development using mouse models and genetics.
Role: The goal of this project is to develop mathematical models and computer simulations of lung tissue development. More specifically, the project will elucidate how cell-cell signaling affects the conducting airways and the distal tip of lung branches during early lung development. The project will require experience in working with ordinary differential equations (ODEs) and/or partial differential equations (PDEs), Newtonian equations of motion and particle interactions, elasticity, three-dimensional geometric objects describing cell shapes, and will likely require developing skills in agent-based cellular dynamics models and/or particle-based tissue mechanics models. The student will need to be able to research, understand, and implement such techniques in a first exploratory phase. The goal will be to identify candidate techniques for a first model that describes growth, patterning, and development of the tissue considering cell proliferation, cell differentiation, and cell migration from the distal tip of an individual lung branch toward the conducting airways.
Qualifications: This project is exclusive to students with a quantitative background who study Physics, Applied Mathematics, Engineering, or Computer Science, for example. An interest in Biology is a plus, but Biology alone without the quantitative background is not sufficient. Ideally, applicants have a solid foundation in coding and mathematical modeling, and an interest in developmental biology, physiology, mathematical biology, and emergent phenomena in tissues. Experience with Python programming is absolutely required and experience with GPU-computing is a big plus. At least 1 day per week is needed to make significant progress, and students who can devote 12 hours or more will be given preference.
Day-to-day supervisor for this project: Jan Christoph, Staff Researcher
Hours: 12 or more hours
Off-Campus Research Site: The first 8 weeks will be on site at the Cardiovascular Research Institute on UCSF's Mission Bay Campus. After the initial training phase, the work can be performed both remotely or, if desired, at our institute. We will have regular 1-on-1 meetings every 1-2 weeks to discuss the progress, either on Zoom or in person, if desired.
Related website: http://cardiacvision.ucsf.edu
Related website: https://cvri.ucsf.edu/people/pao-tien-chuang-md-phd