NCSI: Modeling the Extracellular Matrix using Cellular Particle Dynamics (Apprentice Position)

Status	Completed
Mentor Name	Mahsa Dabagh
Mentor's XSEDE Affiliation	PI
Mentor Has Been in XSEDE Community	1-2 years
Project Title	Modeling the Extracellular Matrix using Cellular Particle Dynamics (Apprentice Position)
Summary	We are developing an in-house code for modeling the extracellular matrix. This matrix has complex structure composed of several components with different size and shape. Distinct type of cells are present and interact with the components. We are aiming to model these dynamic interactions.
Job Description	Student will work on developing in-house code to model the interaction of cancer cells with the components of extracellular matrix. The student is expected to write short Matlab codes and perform required post-processing analysis of the results. The student is expected to participate in regular weekly meetings where challenges and progressions will be discussed in detail. Student is expected to prepare a written report about the project and present it to the mentor at the end of his project. Previous background of the adviser in this regard (one in the PLOS ONE, one in AJP- Heart and Circulatory, and several other journal articles and conference papers) has built a base which will be further developed in this work.
Computational Resources	XSEDE, UWM-HPC center, NSF funded new cluster
Contribution to Community	Our code will have the potential for broadly applicable technology. It can be used to model any multicomponent medium with complex structure. The education and outreach work of this proposal will provide opportunities for underrepresented students to learn about integration of computational modeling in medicine during critical years for forming STEM interest and identity. In addition, to promote participation of female students in graduate studies, research opportunities will be offered from students’ sophomore year onwards.
Position Type	Apprentice
Training Plan	It is anticipated that these aims will yield the following outcomes. First, we will develop a code to simulate dynamic interaction of cancer cells with the components of extracellular matrix. Student will work with a graduate student and one other undergraduate on this project. This will enhance the team working and interdisciplinary work atmosphere for students. Second, student will learn about cancer biology and advanced programming. Third, we plan to write one journal article and one conference paper based on the method developed in this project that will involve the student in preparing these articles as a first experience of scientific publishing.
Student Prerequisites/Conditions/Qualifications	Students with strong interest for coding are encouraged to apply. Familiarity to C++ is preferred.
Duration	Semester
Start Date	09/01/2021
End Date	12/31/2021