Computational Biomechanical Modelling and simulation of cellular migration in heterogeneous 3D environment

Project description

The aim of this project is to develop a simulation framework for the migration of single biological cells in highly constrained heterogeneous 3D environments. This will involve the development of continuum-mechanical models for the cytoplasm and the nucleus as well as coarse-grained models for the cellular cortex and the immersed semi-flexible microtubule fibers.

For the numerical simulation of the cytoplasm flow and of the nucleus, we intend to use novel methods for the numerics of PDEs based on physics-informed neural networks (PINN) which have the potential to serve as robust blackbox tools. Another key challenge will be to address the coupling of the solid structures such as the nucleus and the microtubules to the cytoplasm flow through tools such as the immersed boundary method.

Through this project, we intend to investigate biomechanical aspects of 3D cell migration and to support ongoing research on the transmigration of tumor cells through endothelial layers as well as in the extra-cellular matrix. An important aspect will be to address the question of how the network of microtubule fibers regulates various aspects of cell migration such as nuclear plasticity and cortical actomyosin contractility during constrained migration.

Outcomes

The projected outcomes of this project involve

1. The formulation of a closed biomechanical model for single-cell migration in 3D,
2. Implementation of an efficient and robust numerical scheme for the PDEs (Stokes Flow, visco-elastic models for the nucleus) arising in cellular biomechanics,
3. A simulation framework for the migration of single biological cells in constrained environments,
4. Computational investigation through a hybrid approach of machine learning and scientific computation to understand the regulatory mechanisms during constrained cell migration.

Essential capabilities

Programming (computational science), (Applied) Mathematics, Physics (Computational Mechanics).

Desireable capabilities

Interest in and understanding of fundamental aspects of cellular biomechanics.

Expected qualifications (Course/Degrees etc.)

Mathematics, Physics, Engineering (with interest in computational mechanics and modelling focus from Comp Sci, Mechanical, Civil, Aero, Biomedical etc).

Additional information for applicants

note: i-students must have own scholarship to apply (CSIR, UCG-NET, etc)