*EASTBIO* Particle-based computational platform for the simulation of Brownian reactive dynamics of proteins.

The search for a mesoscopic description of biological systems is necessary because microscopic description, such as molecular dynamics, cannot handle large systems, while continuous mean-field description, such as reaction-diffusion partial differential equations, fails to incorporate the particulate nature of molecules. Frequently, in biological systems, reactions between large molecules, such as proteins and their complexes, are strongly affected by their ability to physically encounter each other by diffusive motion, which is hampered by molecular crowding. These limitations, without exclusion, apply to all cases of self-assembly of viral particles, organelles, etc.

The aim of this project is to build a coarse-grained particle-based approach for the simulation of Brownian reactive dynamics of large biological molecules and their complexes. The student will use LAMMPS, an open-source community-developed package for molecular dynamics, to develop methods for modelling of protein-protein interactions, chemical reactions between proteins, and, ultimately, self-assembly of large spatially-complex cellular structures, such as centrosomes. Biophysical principles that govern formation of cellular organelles, which are not delimited by a membrane, such as nucleolus, stress granules, centrosomes and kinetochores, have recently attracted much attention in biology and physics. A continuous theory based on equilibrium phase-separation has been suggested, but it does not explain several important experimentally observed biological phenomena, such as rapid dynamic exchange of organelle components with the cytoplasm.

This project offers an opportunity for an enthusiastic and motivated student with the background in physics, chemical engineering or applied mathematics to build up their knowledge in biology, molecular biophysics, develop new skills in scientific programming and biomolecular simulation. The supervisors of the project have proven expertise and extensive track record in biology, physics and scientific programming. The student will be supported by expert technical and scientific advice but is expected to actively drive their own project.