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Project B3: Coarse-graining of solvent effects in force-probe molecular dynamics simulations The study of the conformational kinetics of biomolecules and supramolecular complexes using molecular simulations often is complicated by the fact that these processes are very slow. Various simulation techniques have been developed in order to resolve this issue. One very efficient way to investigate the atomistic details of conformational changes is provided by force-probe molecular dynamics (FPMD) simulations. In the most common realization of this technique, one end of the (supra)molecular system under consideration is fixed in space and the other end is pulled apart with a constant velocity via the application of a harmonic potential. From the distributions of the forces needed to unfold the system important information regarding the kinetics and the thermodynamics of the relevant conformational rearrangements can be obtained via a statistical analysis. The direct comparison to the results of experimental realizations of force spectroscopy […]

Project B5: Multi-resolution methods including quantum chemistry, force fields, and hybrid particle-field schemes Multiscaling techniques that involve a quantum-chemical treatment of the electronic structure for the part with the highest resolution are promising computational tools. They are particularly useful for dealing with problems involving large systems like enzymes, membranes, polymers, etc., where, for example, chemical reactions take place. Having completed in the previous funding period of the TRR (i.e., the first funding period of this project) a corresponding QM/MM implementation that allows to include high-accuracy quantum-chemical methods from either coupled-cluster (CC) theory (i.e., CCSD, CCSD(T), etc.) or of multiconfigurational nature (i.e., CASSCF), we intend to complete the envisioned QM/MM/CG/hPF implementation that extends the QM/MM approach to coarse-grained (CG) treatments. In particular, we plan on using hybrid particle-field (hPF) theory based on its Hamiltonian reformulation, where the latter has been accomplished in the first funding period of this project. This reformulation […]