TY  - GEN
CY  - Heidelberg
AV  - public
Y1  - 2023///
TI  - Coarse-grained molecular dynamics of semi-flexible (bio-)polymers under force
ID  - heidok34108
A1  - Brosz, Matthias Julian
UR  - https://archiv.ub.uni-heidelberg.de/volltextserver/34108/
N2  - Living organisms build upon semi-flexible biopolymers to confer structural integrity and functionality to cells. Semi-flexible (bio-)polymers assemble into hierarchical networks governed by an interplay between entropic and enthalpic effects. The assembled network features a non-linear response to mechanical load, like strain-stiffening and compression-softening. This non-linearity stems from the many-body nature at the microscale, which significantly influences the behaviour at the mesoscale. Due to the lack of non-generic scale-bridging models, the response of semi-flexible (bio-)polymer networks to mechanical stress is not yet fully understood. The aim of this thesis is thus to explore major molecular deformation mechanisms of semi-flexible (bio-)polymer networks by large-scale yet chemically informed molecular dynamics simulations. We developed coarse-grained models for two semi-flexible (bio-)polymers with similar persistence lengths, namely poly(para-phenylene ethynylene)s (PPEs) and collagen, using the Martini 3 force field to perform molecular dynamics simulations under force and to identify locations of high-force concentration with bonds being prone to rupture. Our Martini 3 models largely capture key structural, mechanical and thermodynamic observables from atomistic simulations and experiments from the literature, including interchain packing, mechanical bending stiffness and solvation properties. We show that the entanglement of PPEs in large-scale bulk assemblies increases with polymer chain length. We further observe that long-chain PPE networks under shear-flow form shear bands with extreme shear rates in the fast band, that is, where rupture forces are highest and bonds are likely to fail. Also, we built atomistic structural models for collagen microfibrils with a tuneable crosslink density and combined Martini 3 with G?-like potentials to find an increase in microfibrillar stretching with decreasing number of crosslinks. Our Martini 3 collagen model is suited to capture the force-stretching of collagen microfibrils from all-atom simulations, performed in collaboration with the Riken institute in Kobe. The two newly developed coarse-grained models for the semi-flexible PPE and collagen complement experiments by predicting bond rupture events in the large-scale assembled polymer networks. They push the frontier of molecular dynamics simulations more close to realism, that is, to their actual biological or synthetic counterparts, and will in future allow probing micrometer sized systems of various structural configurations.
ER  -