Molecular dynamics (MD) method and agent-based model (ABM) in simulation of stem cell deposition on the surface with nanopattern: Current development stage of an in-house simulator

Observations that the differentiation of stem cell into other cells, e.g. bone cell, blood cell, epithelial cell, muscle cell, nervous cell, are well known. In the recent years experiment of deposition of stem cell on a surface with nanopattern has been succesfully showing the difference of produced cells. The patterns can be in the form of nanopillar, nanowells, or other form in between. The order of magnitude of the nanostructure compared to the cell size plays also importance role, in which scale that the pattern can influence the cell, e.g. internally, externally, or until the shape of the cell colony. Single cell based on granular model is simulated using molecular dynamics (MD) method, where the content of the cell is approximated using agent-based model (ABM) to assure that the cell volume is kept constant. Due to cell shape change induced by the nanopartern, interaction between cell inner particles, performed by agents, has also changed. In this article we are reporting the development stage of an in-house simulator.