Optimization of cryopreservation protocols

Cryopreservation is the process of cooling and storing biological samples at very low temperatures. One of the biggest challenges we face is the successful cryopreservation of whole organs; a practise that would allow for prolonged storage and safer transportation. We face several challenges when attempting to cryopreserve organs, such as osmotic damage, solution toxicity and ice formation. We created a moving boundary tissue model to describe the loading of cryoprotective agents (CPAs) to aid in the optimized design of experimental protocols.

Multiscale modeling of tumour morphology

Local cancer cell invasion is a complex multiscale process that combines the secretion of matrix-degrading enzymes (MDEs) with a series of altered key cell processes, to degrade important components of the surrounding extracellular matrix (ECM) and this way spread further in the healthy tissue. We constructed a model to describe the interactions between cancer cells and the surrounding ECM, incorporating the underlying fibre network and cell adhesion dynamics. We explored the impact on cancer invasion patterns of different levels of cell adhesion in conjunction with continuous ECM fibres rearrangement.

Agent-based modeling of zebrafish skin patterns

Zebrafish feature black and yellow stripes, while mutants display different patterns. These patterns arise from self-organizing interactions of pigment cells. Using a prior agent-based model, we delved deeper into the mechanisms of these interactions by adapting the model to account for stochastic communication between cells. The aim is to develop a more realistic model of cellular interactions by incorporating cellular protrusions and diffusing signals from individual cells.

Microenvironment model development

The extracellular environment is a key contributor to many biological systems; however, it is a highly complex structure and can be difficult to describe within a mathematical model. Using the computational package PhysiCell, we aim to develop an add-on, PhysiMeSS, that will enable the user to incorporate specific components of the ECM, along with all of their associated dynamics, to their model.