Computational Biophysics

SMMLab research activity on computational biophysics is done within the Center for Complexity and Biosystems in in close collaboration with the group of Caterina La Porta.  We are pursuing collaborative research on a variety of topics such as cell division, the biomechanics of cells and tissues, protein aggregation in neurodegenerative diseases, population dynamics of cancer cells, simulation and analysis of pathways.

The physics of Cancer:

We using mathematical and physics based model to study cancer.  We have devised a model of cancer stem cell population dynamcis to study cancer growtn and senescence and compared the results with experiments. We have studyied  mathematical models the role of cancer stem cell markers and simulated individual particle models for tumor growth.  We have also worked on collective migration of cancer and developed computational models and image analysis tools.

Our work is summarized in a textbook  (written with C. La Porta) : “Physics of Cancer” published by Cambridge University Press.

 

 

Models for cell division:

MTWe worked on the dynamics of microtubules, developing a mechanical model for their polymerization and depolymerization dynamics. Microtubules represent an impressive example on the way a mechanical process, in this case the change of the intrinsic curvature of protofilaments during depolymerization, drives a biological function. Other contributions to this field include the modeling chromosome segregation, the microtubule-kinetochore interface and motor dynamics on microtubules.

 

Key publications:
A. Taloni, E. Kardash, O. U. Salman, L. Truskinovsky, S. Zapperi, and C. A. M. La Porta “ Volume Changes During Active Shape Fluctuations in Cells” Phys. Rev. Lett. 114, 208101 (2015).
Z. Budrikis, G. Costantini, C. A. M. La Porta, S. Zapperi, “Protein accumulation in the endoplasmic reticulum as a non-equilibrium phase transition” Nature Comm. 5, 3620 (2014).
Z. Bertalan, C. A. M. La Porta, H. Maiato, S. Zapperi, Conformational mechanism for the stability of microtubule-kinetochore attachments. Biophysical Journal, 289–300 (2014).