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I am trying to understand how cell to cell communication is studied using a discrete modelling framework. Could someone please suggest suitable references or libraries which already have implementations of this? I have come across continuum-based approaches which treat tissue mass as a homogeneous medium but I am looking for a discrete approach.

I want to understand how the diffusion of drug molecules can be expressed in equations to study the passive transport from one cell domain in tissue to the adjacent cell domain.

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It sounds to me there are two things you want to model/simulate that live on different length scales. Molecular diffusion of any drug agent or signaling molecule can indeed be simulated discretley via molecular dynamics (MD) simulations. There, you simulate the positions, velocities and interactions of single molecules and may observer how they diffuse or react etc. example

If you want to simulate the behaviour of biological cells, you may do so too enter link description here. The problem is propably that cells are orders of magnitude larger than single molecules, and you will have a hard time simulating both of them at the same time ("multiscale problem").

(If your cells do not move and stick together in tissue, and you want to simulate the diffusion through their interfaces then you can still simulate the problem continuously, but you alter the permeability at the cell interface accordingly.)

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