Andrea Grafmüller

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Fusion of bilayer membranes is studied via dissipative particle dynamics (DPD) simulations. A new set of DPD parameters is introduced which leads to an energy barrier for flips of lipid molecules between adhering membranes. A large number of fusion events is monitored for a vesicle in contact with a planar membrane. Several time scales of the fusion process(More)
The fusion of lipid bilayers is studied with dissipative particle dynamics simulations. First, to achieve control over membrane properties, the effects of individual simulation parameters are studied and optimized. Then, a large number of fusion events for a vesicle and a planar bilayer are simulated using the optimized parameter set. In the observed fusion(More)
The complex polymerization dynamics of the microtubule (MT) plus end are closely linked to the hydrolysis of the GTP nucleotide bound to the β-tubulin. The destabilization is thought to be associated with the conformational change of the tubulin dimers from the straight conformation in the MT lattice to a curved conformation. It remains under debate whether(More)
Microtubule (MT) stability is related to the hydrolysis of the guanosine triphosphate nucleotide (NT) bound to β-tubulin. However, the molecular mechanism by which the NT state influences the stability of the contacts in the MT lattice remains elusive. Here, we present large-scale atomistic simulations of different tubulin aggregates, including individual(More)
Understanding the factors that influence the free energy of lipids in bilayer membranes is an essential step toward understanding exchange processes of lipids between membranes. In general, both lipid composition and membrane geometry can affect lipid exchange rates between bilayer membranes. Here, the free energy change ΔG(des) for the desorption of(More)
Coarse-grained (CG) models of large biomolecular complexes enable simulations of these systems over long timescales that are not accessible for atomistic molecular dynamics (MD) simulations. A systematic methodology, called essential dynamics coarse-graining (ED-CG), has been developed for defining coarse-grained sites in a large biomolecule. The method(More)
Membrane nanopores are central players for a range of important cellular membrane remodeling processes as well as membrane rupture. Understanding pore formation in tense membranes requires comprehension of the molecular mechanism of pore formation and the associated free energy change as a function of the membrane tension. Here we propose a scheme to(More)
We present a procedure to obtain Coarse-Grained (CG) models for aqueous polysaccharide solutions that are transferable over different degrees of polymerization and different polysaccharide concentrations based on atomistic Molecular Dynamics (MD) simulations. This is achieved by a hybrid procedure combining Boltzmann Inversion (BI) and the Multiscale(More)
Computational models can provide detailed information about molecular conformations and interactions in solution, which is currently inaccessible by other means in many cases. Here we describe an efficient and precise coarse-grained model for long polysaccharides in aqueous solution at different physico-chemical conditions such as pH and ionic strength. The(More)