BME PhD Preliminary Exam Announcement for Ryan Speitel (T. Kinzer-Ursem, advisor)

Everyone is invited to attend the public presentation beginning at 11:00 am.

Title: Addressing Challenges of Probing Calcium-Dependent Signaling Systems by Developing a Dynamic, Hybrid, and Multiscale Framework

Date/Time: April 30th, 11:00am

Location: DLR 131 or

Zoom - https://purdue-edu.zoom.us/meeting/register/U-pFyvjQRSun0RBk5gAT2w

Committee: Tamara Kinzer-Ursem (PI), Elsje Pienaar, Phillip Pare, Alejandra Magana

Abstract:

Calcium-dependent signaling plays a crucial role in the regulation of key biological functions, such as fertility, cardiac health, and memory formation.  However, current methods struggle to capture how localized calcium dynamics scale to cellular and tissue level outcomes. Traditionally, researchers have used computational modeling frameworks, including MCell, VCell, and SMART, to model subcellular signaling. These frameworks allow simulating complex biological systems and signaling dynamics but face computational bottlenecks at larger spatiotemporal scales. 

This highlights a key challenge, as how do we develop an efficient calcium-dependent signaling model while preserving the required fidelity to capture how small changes in system components or calcium signaling dynamics lead to large differences in cellular and tissue states.

We propose a hybrid, dynamic, and multiscale modeling framework that integrates several mechanistic modeling techniques, enabling on the fly adjustments to model resolution, balancing mechanistic detail and computational efficiency. Our approach addresses difficulties in hybrid modeling  by introducing a holistic data architecture, transitional algorithms, and a generalized opinionated framework. In combination, these tools enable the rapid development and exploration of complex multiscale systems and unlock avenues for state driven surrogate model development. The preliminary utility of these methods has been demonstrated using a hybrid model of diffusion in a single subcellular unit.  By enabling scalable, efficient multiscale simulations, this framework will enhance research into calcium-dependent disorders, including cardiovascular and neurodegenerative diseases.