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Computer modeling of diffusional transport in hydrogel
 Koláček, Jakub ; Sedláček, Petr (referee) ; Pekař, Miloslav (advisor)
This thesis focuses on the design of models applicable to the simulation of particle motion in a viscoelastic environment in COMSOL Multiphysics. Two approaches have been chosen for the design of these models: the first is the design of a geometry representing the porous structure of hydrogels and the second is the implementation of viscoelasticity using the mathematical concept of a continuous environment. Two elementary geometrical models are presented in this work – a three-dimensional periodic lattice and a spherical volume model. Furthermore, the possibilities of implementing the generalized Langevin equation in COMSOL Multiphysics are explored by using the interface for custom partial differential equations, by adding an auxiliary dependent variable, or by defining a custom external function written in the C language. The proposed geometric models did not prove to be suitable for the simulation of viscoelastic environment. An implementation using an external function seems to be the most promising, as it offers the most customization possibilities, and its implementation reflects the theoretical foundations. The thesis also includes a custom add-in written for COMSOL Multiphysics to facilitate the evaluation of simulation data and a modified Python script to calculate the complex shear modulus from MSD data.
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