We develop physics-based mathematical models for soft biological structures to elucidate the fundamental physics underlying their dynamic behavior. Research interest examples include dynamics of viruses injection machines, cytoskeletal biofilaments, DNA folding, bacterial swimming, ciliary motion, etc. Below are some sample projects.
Multi-body dynamics of injection machinery of contractile viruses
The virus bacteriophage T4 infects the bacterium Escherichia coli using an intriguing nanoscale injection machinery that employs a contractile tail. The injection machinery is responsible for recognizing and puncturing the bacterial host and transferring the viral genome into the host during infection. Using a combination of atomistic and continuum representations, we develop a system-level model of the entire bacteriophage T4 interacting with a host cell. Our dynamic model exposes the energetics, forces, and dynamical pathway associated with the injection process. The results have further implications for future nanotechnology devices for DNA transfection and experimental phage therapies.
Related publications:
- Maghsoodi, A., Chatterjee, A., Andricioaei, I., Perkins, N., 2019, “How the Phage T4 Injection Machinery Works including Energetics, Forces, Pathway and Time Scale”, Proceedings of the National Academy of Sciences of the United States of America (PNAS), 116(50), pp.25097-25105. Article Link.
- Maghsoodi, A., Chatterjee, A., Andricioaei, I., Perkins, N., 2017, “Dynamic Model Exposes the Energetics and Dynamics of the Injection Machinery for Bacteriophage T4”, Biophysical Journal, 113(1), 195-205. (Featured as New and Notable Research Article in Biophysical Journal). Article Link.
- Maghsoodi, A., Chatterjee, A., Andricioaei, I., Perkins, N., 2016, “A First Model of the Dynamics of the Bacteriophage T4 Injection Machinery”, Journal of Computational and Nonlinear Dynamics, 11 (4). Article Link.
- Chatterjee, A., Maghsoodi, A., Perkins, N., Andricioaei, I., 2019 “Elastic Continuum Stiffness of Contractile Tail Sheaths from Molecular Dynamics Simulations”, Journal of Chemical Physics, 151, 185103. Article Link.
Viscoelastic properties of thermally fluctuating biofilaments
Thermally fluctuating biofilaments possessing porous structures or viscoelastic properties exhibit energy losses from internal friction as well as external friction from drag. We develop a new energy dissipation model that captures the important effects of dynamic shear and bending. Our new model yields superior estimates of energy dissipation for fluctuating biofilaments such as DNA, RNA, and microtubules. Particularly, our model captures the effect of shear in addition to bending and can be used for both short and long biofilaments experiencing a combination of shear and bending deformations.
Related publications:
Maghsoodi, A., Perkins, N., 2018, ”Shear Deformation Dissipates Energy in Biofilaments”, Scientific Reports, 8(1). Article Link.