implementing agent-based model for Dynamic Cellular Simulations for Fibrosis

Principal Investigator: Dr. Luis Sordo Vieira

Institution/Department: University of Florida, College of Medicine

Length of Project: September 2023 - PRESENT

Agent-based Model

The integration of Agent-Based Modeling (ABM) with Ordinary Differential Equations (ODEs)
presents a powerful approach for simulating complex multiscale dynamics in various biological
systems. My research based on simulation results of the multiscale model will likely allow one to find families of parameters of the ODE component that result in the observed simulation result and whether those parameters are biologically relevant.

Logic Based Model

We have successfully implemented a previously published multiscale model of fibrosis that incorporates an intricate ODE model for the intracellular component (shown on the left). This model will integrate with the ABM in order to capture the intracellular dynamics of individual cells. Our current focus is on independently implementing and improving upon the ABM component given with the publication.

Ultimate Goal

Our ultimate goal is to explore the families of parameters that lead to relevant simulations using an autoencoder, a type of neural network that encodes and decodes the input data. This will allow us to explore the biological significance of such parameters by comparing to previous literature and experimental collaborators. Overall, our work aims to advance understanding of fibrosis progression and provide insights into potential therapeutic interventions through computational modeling approaches.

Model Paper

Here are some of the model papers we are utilizing and improving upon: https://www.sciencedirect.com/science/article/pii/S0022282816300554#bb0045

https://www.frontiersin.org/journals/physiology/articles/10.3389/fphys.2019.01481/full