Molecular simulations of reversible mechanical unfolding and of phospholipid bilayers
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Abstract
This thesis reports simulations of the mechanical properties of reversibly unfolding calix[4]arene-catenanes (part I) and of the phase behavior of phospholipid bilayers (part II).
Part I comprises detailed studies of reversible force probe molecular dynamics (FPMD) simulations of calix[4]arene-catenanes as sophisticated model systems. A special focus is on the dependence of FPMD simulations on the pulling parameters, i.e., the force constant K and the pulling velocity V. In most existing models for the interpretation of such simulations, only the loading rate, µ = KV, is considered but not the individual values of K and V. In addition these models are strictly limited to irreversible systems. Here, a new model for reversible systems which explains all the characteristic rupture and rejoin forces is presented. Furthermore, detailed studies concerning the transition rates from the closed into the open states are presented and are verified by kinetic Monte Carlo simulations.
In part II one-component and two-component phospholipid bilayers, so-called reconstituted lipid bilayers, are studied. These systems offer a deep insight into the properties and behavior of lipids on a coarse-grained (CG) level. In this work the CG model of the phospholipids 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) are studied extensively using different MD approaches. The main focus of this work is on the phase behavior of these lipids. Through this work, a new parametrized CG model of the unsaturated DOPC is introduced. It is based on the CG MARTINI model but unlike the original model it is able to reproduce the liquid-to-gel transition in semi-quantitative agreement with the experimental data. Furthermore, the well-studied CG model of DPPC is investigated with the particle-field (PF) approach. These approaches take the CG model as a basis for further approximations and offer a significant speed-up of the simulations but they are less accurate. Nonetheless, these approaches are an important step towards the simulation of mesoscale systems. Lastly, a new cholesterol model is presented which is able to reproduce the liquid-ordered phase using the PF approach.