Development of novel computational tools and algorithms for realistic 3D visualization and modeling of non-membranous cellular organelles

Recently much effort has been invested in understanding the organization of cellular structures that are not delimited by membrane, very small (~100 nm) in size and formed by dense packing of dozens of protein types, such as kinetochores and centrioles. This recent interest is fuelled by the growing recognition that these structures play not only structural but also crucial signaling functions, for example, in the control of the spindle assembly checkpoint and mitotic exit network. Presently, biophysical understanding of these essentially semi-dense protein crystals is very rudimentary. To improve it, computational tools allowing 3D visualization and simulation are absolutely required.

This highly interdisciplinary project that is positioned on the interface of computer science, physics and biology has an ambitious goal to adapt and further develop tools that will allow both realistic 3D visualization and modeling. A student who is expected to possess background and experience in mathematics and programming will work with the open-source platform CellPack (www.cellpack.org) with the specific aim to develop realistic spatial models for the kinetochore and spindle pole body (fungal centrioles). The developed spatial static models will be used to interface with physical methods of dynamical simulation, such as molecular dynamics and Brownian particle dynamics. These methods have been burgeoning recently, and our collaborators at the U of E physics have a strong background in applying LAMMPS molecular dynamics platform to simpler and more conventional biological systems, such as lipid membranes and chromatin.

This project will provide a unique opportunity for a student with the background in mathematical sciences to develop novel skills and knowledge of modern cell biology. The project is expected to have strong synergy with the research contacted in the Wellcome Trust Center for Cell Biology in Edinburgh as well as with the research of our collaborators at the University of Dundee.