Virtual Cell model: The first biophysical to map ECM to chromatin configuration(2017)

Development of a Virtual Cell Model to Predict Cell Response to Substrate Topography, during my master’s degree study, introduced a computational framework for predicting how cells respond to engineered surface features before extensive experimental testing. The work addressed a central problem in biomaterials and cell engineering: although cells are highly sensitive to physical cues such as surface topography and mechanics, designing substrates has often relied on costly trial-and-error experimentation. In this study, I helped develop a multicomponent virtual cell model that links substrate topography to chromatin organization through multiple scales of simulation, spanning whole-cell shape, cytoskeletal organization, nuclear deformation, and chromatin configuration. The model predicts changes in cell and nuclear behavior on different substrates, including cell shape, orientation, and higher-order nuclear organization, and was compared with cell-culture experiments to capture the qualitative behavior of mesenchymal stem cells across engineered environments. More broadly, this work aimed to move substrate design from empirical screening toward predictive modeling. By connecting material topography to cell-scale and nuclear-scale structural responses, it proposed a faster and more systematic route for engineering surfaces for stem cell control and related biomedical applications.

Read more: https://pubs.acs.org/doi/10.1021/acsnano.7b03732

Code at: https://github.com/TiamHeydari/virtual_cell_cpp

Patent ar: https://patentimages.storage.googleapis.com/8a/e2/41/a60b60e43d2d80/US20180196914A1.pdf

VC’s application in luripotent Stem Cell-Derived Cardiomyocytes:https://advanced.onlinelibrary.wiley.com/doi/abs/10.1002/adfm.201707378