Simulations of biopolymer networks under shear

Doctoral Thesis

In this thesis we present a new method to simulate realistic three-dimensional networks of biopolymers under shear. These biopolymer networks are important for the structural functions of cells and tissues. We use the method to analyze these networks under shear, and consider the elastic modulus, the non-affinity during deformation, the normal modes and the density of states. We expand our analysis to composite networks consisting of stiff and floppy filaments. In the final chapter of the thesis we incorporate the thermal and viscous interactions of the surrounding medium in the calculations, and present the results of the simulations of the shear frequency dependence of the network response. We find that non-affine reorientations are important for understanding the network response. These non-affine reorientations make the networks relatively soft under shear and delay the onset of stiffnening. In composite networks non-affine reorientations allow for an intricate interplay between...Show moreIn this thesis we present a new method to simulate realistic three-dimensional networks of biopolymers under shear. These biopolymer networks are important for the structural functions of cells and tissues. We use the method to analyze these networks under shear, and consider the elastic modulus, the non-affinity during deformation, the normal modes and the density of states. We expand our analysis to composite networks consisting of stiff and floppy filaments. In the final chapter of the thesis we incorporate the thermal and viscous interactions of the surrounding medium in the calculations, and present the results of the simulations of the shear frequency dependence of the network response. We find that non-affine reorientations are important for understanding the network response. These non-affine reorientations make the networks relatively soft under shear and delay the onset of stiffnening. In composite networks non-affine reorientations allow for an intricate interplay between the stiff and floppy filaments. The frequency-dependent response shows a transition from a soft, non-affine regime at low frequencies to a stiff, close-to-affine response at high frequencies.Show less

Biopolymer networks

Cytoskeleton

Elastic modulus

Non-affinity

Simulations