HRP SU20-20: Research Opportunity with Dr. Masoud Nickaeen

Project Mentor

Dr. Masoud Nickaeen
Center for Cell Analysis and Modeling (Department of Cell Biology)

Undergraduate Research Opportunity Description

Project Description We will develop algorithms to numerically solve partial differential equations in domains with moving boundaries. We will implement these algorithms in computer programs and run simulations to evaluate their accuracy and validity. We will benchmark the utility of the new algorithms in the study of cellular processes that lead to or rely on the motion and deformation of the cells, their organelles or subcellular structures.
Project Direction We are interested in developing a computational framework for dynamic spatial modeling of cell shape changes and migration. These models will be used to mechanistically investigate shape changes of a broad class of cellular processes such as endocytosis, cytokinesis and cell migration. The algorithms developed during this project will be eventually incorporated into the VCell ( software to make them accessible to the cell biology research
Mentorship and Supervision Mentorship and Supervision Plan
We will talk about the project in detail and identify their research strengths and weaknesses at the beginning of the program. When familiarity with a specific subject is not enough to carry out the research project, I will give them a crash course on the subject for a short period (1-2 weeks) and closely monitor their progress. I’ll take the following steps to maximize their learning in this period:
– Introduce chapters from related textbooks, I’ll make sure these books are appropriate for people with small or no relevant background, and teach them the chosen material in a classroom setting
– Give them exercises to assess their learning during the course
– Provide additional references for a deeper understanding of more complex concepts
From here on, the key to a successful collaboration is to establish a good relationship with them, by being accessible and responsive for their questions/concerns. They will have clear instructions/plans for each week and their progress will be assessed at the end of that week. I will encourage them to think about challenging problems on their own, but will guide them along the way to help them make the necessary progress to keep them motivated for doing research.
They will have the opportunity to interact with other graduate and undergraduate students in the center. Also, I’ll encourage them to participate in weekly Research in Progress or Journal Club presentations by our Faculty and research staff, who have similar biomedical research interests that could help broaden the student’s viewpoints on the subject.And finally, we will follow all instructions required by The Office of Undergraduate Research to assess and provide feedback for the student’s progress during this program.
Student Qualifications Research Interest:
computational methods for solving partial/ordinary differential equations
cell biology, mechanics of cellular processes and biochemistry
algorithm development
transport phenomenaCoursework:
Linear algebra, calculus, partial/ordinary differential equations, computer programming, numerical analysis

Other skills:
Matlab, Finite Volume Method, Mesh Generation

Summer Schedule Options Research Dates: May 26 to July 31, 2020
Schedule: M-F, 9am-5pm
Project Continuation Fall 2020, Spring 2021
Academic Year Time Commitment 3-6  hours/week
Possible Thesis Project Yes


Submit an online application for this research opportunity at The application deadline is Monday, February 3, 2020.

This application requires a cover letter, an unofficial transcript and a brief statement of research interests.