Theoretical and computational modeling of the dynamics of multicellular and lipid membrane systems
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This dissertation presents two research projects that apply theoretical and computational modeling to (1) describe and predict the formation and shape evolution of three-dimensional (3D) bioprinted tissue constructs, and (2) investigate the effect of a silica substrate on the structural and dynamic properties of a single fully hydrated lipid bilayer. (1) Bioprinting, a novel tissue engineering technique, has the ultimate goal of using 3D printers with bioink made from a person’s own cells to create tissues in the laboratory for transplantation or drug testing. The outcome of the post-bioprinting process, where the bioink particles fuse to form the desired 3D tissue construct, is difficult to predict and experimental techniques have generally been optimized through trial and error. To address this shortcoming, by employing theoretical modeling and computer simulations, we have developed and implemented an effective procedure that is capable of describing and predicting the shape dynamics during post-printing structure formation in 3D bioprinting. In particular, we have explained and demonstrated that the post-printing fusion process is considerably faster when using cylindrical instead of spheroidal bioink particles, a result that has considerable practical implication for extrusion bioprinting. (2) The study of lipid bilayers using neutron scattering experiments requires samples that contain a large stack of membranes. The analysis and computer simulation of such systems is challenging mainly due to the unknown amount of water separating the membranes. To overcome this difficulty, more recent experiments place single lipid membranes onto a support and stack about a hundred of them together. In this project we use molecular dynamics simulations of both free-standing and hydrated single-supported lipid bilayers to investigate the effect of the silica substrate on the structural and dynamical properties of the lipids and hydration waters. Our results may provide useful information in interpreting some recent neutron scattering experiments.