BioDynaMo collaboration

 The central nervous system is a vast and complex assembly of neurons responsible for information integration, resulting in an astonishing variety of phenotypic responses. Understanding how this highly complex structure emerges from a few progenitor cells that self-organize represents one of the biggest challenge to modern neuroscience. To reach this goal, computational neuroscience and modelling have become an increasingly used tool during the past decades. By being able to model both cell bodies and neurites (dendrites and axons) growth self organisation, BioDynaMo is particularly well suited to conduct neural tissue developmental studies. By representing neurites as a chain of small cylinders attached to a cell body, it is possible to precisely model dendritic and axonal arbours. Validation can be done by comparing these simulated neurons with real morphologies obtained during in-vitro experiments. Metrics such as the arbour length and diameter, the number of branching point or ...

 BioDynaMo provides an excellent basis for the modelling of cells responding to cooling and thawing during cryopreservation, this is due to BioDynaMo’s ability to create agent based simulations where by each individual cell can act independently of those around it based on local environmental factors. Currently through the use of behaviors within BioDynaMo, one can simulate a cells osmotic response to changes in temperature for 0°C and below for multiple cooling rates. This is modelled as a change in the volume of the cell, which can then be interpreted by the chemical diffusion grid as water diffusing into the extracellular medium , in the case of cooling, and increase the concentration around the cell accordingly. The concentration grid will then diffuse the water throughout the remaining extracellular space at each time step of the simulation. At current there is a Thermodynamics module being developed to accompany the behaviors for cellular behaviour and chemical diffusion, whi...