UBC Math Bio Seminar: Dr. James Glazier's Visit and Graduate Presentations

Join us for a unique opportunity to meet and learn from Dr. James Glazier, a pioneer in computational biology and a renowned cell and tissue modelling expert. Dr. Glazier’s visit will feature a full day of activities, including a showcase of our graduate students' cutting-edge research and a keynote presentation by Dr. Glazier himself. This event is open to all interested in the dynamic intersections of biology, physics, and computational modelling.

Abstract:

The development, homeostasis, and dysfunction of tissues emerge from the interactions between cells, their extracellular environment, and the molecular signals that regulate them. Virtual Tissues are physics-based, multi-scale, agent-based models designed to simulate the behavior of cells and tissues. A common computational methodology for describing cell dynamics in these Virtual Tissue models is the Cellular Potts Model (CPM), also known as the Glazier-Graner-Hogeweg (GGH) model. This approach originated from the Potts Model, a generalization of the Ising model developed in the 1950s to describe magnetization phenomena in ferromagnetic materials. This methodology was initially extended by Grest, Srolovitz and Anderson at Exxon Research to model the coarsening of metallic grains and liquid foams and then by Glazier and Graner to model the dynamics of biological cells, which adjust their shape and configuration to minimize their effective energy and by Hogeweg to include chemotaxis (the movement of cells in response to external chemical fields). In the CPM/GGH model, cells are represented as domains of lattice points, and their interactions are governed by effective energy terms that reflect biological properties such as adhesion, volume constraints, and motility. This flexible and extensible framework allows for the simulation of complex multicellular processes such as cell migration, aggregation, and tissue formation. The CPM/GGH model has been widely used to study morphogenesis, tumor growth, angiogenesis, wound healing, engineered tissues, toxicological effects, infectious diseases, and immune responses. I will discuss the strengths and limitations of this approach and illustrate its use in the context of simulations of angiogenesis and their extensions in cancer and retinal modeling.

You can download CompuCell3D from https://compucell3d.org/SrcBin 

For a list of recent papers published using CompuCell3D (ranging from toxicological perturbations of chicken embryonic development to the role of estrogen in muscle recovery after injury) see: https://compucell3d.org/Publications