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B3: Coarse-graining of solvent effects in force-probe molecular dynamics simulations

The goal of this project is to develop multiscale schemes for efficient force probe molecular dynamics (FPMD) simulations. In all-atom (AA) simulations, pulling velocities are typically 6-8 orders of magnitude larger than in experiments. We develop hybrid schemes with an AA description for the solute and a coarse-grained (CG) procedure for the solvent to speed up FPMD simulations. In the first funding period, we have considered aprotic solvents and used Markov-state models for further dynamical coarse-graining. In the future, we plan to develop methods that allow to study also protic solvents and apply them to study molecular complexes that unfold via stable intermediates, such as calix[4]arene catenane dimer and foldamers.


Structural Origin of Metal Specificity in Isatin Hydrolase from Labrenzia aggregata Investigated by Computer Simulations
Lalita Uribe, Gregor Diezemann, Jürgen Gauss, Jens Preben Morth, Michele Cascella
Chemistry - A European Journal 24 (20), 5074-5077 (2018);
doi:10.1002/chem.201705159

Intramolecular structural parameters are key modulators of the gel-liquid transition in coarse grained simulations of DPPC and DOPC lipid bilayers
Stefan Jaschonek, Michele Cascella, Jürgen Gauss, Gregor Diezemann, Giuseppe Milano
Biochemical and Biophysical Research Communications 498 (2), 327-333 (2018);
doi:10.1016/j.bbrc.2017.10.132

Force probe simulations using a hybrid scheme with virtual sites
Ken Schäfer, Marco Oestereich, Jürgen Gauss, Gregor Diezemann
The Journal of Chemical Physics 147 (13), 134909 (2017);
doi:10.1063/1.4986194

Force probe simulations of a reversibly rebinding system: Impact of pulling device stiffness
Stefan Jaschonek, Gregor Diezemann
The Journal of Chemical Physics 146 (12), 124901 (2017);
doi:10.1063/1.4978678

Determining Factors for the Unfolding Pathway of Peptides, Peptoids, and Peptidic Foldamers
Lalita Uribe, Jürgen Gauss, Gregor Diezemann
The Journal of Physical Chemistry B 120 (40), 10433-10441 (2016);
doi:10.1021/acs.jpcb.6b06784

Mechanical unfolding pathway of a model β-peptide foldamer
Lalita Uribe, Stefan Jaschonek, Jürgen Gauss, Gregor Diezemann
The Journal of Chemical Physics 142 (20), 204901 (2015);
doi:10.1063/1.4921371

Comparative Study of the Mechanical Unfolding Pathways of α- and β-Peptides
Lalita Uribe, Jürgen Gauss, Gregor Diezemann
The Journal of Physical Chemistry B 119 (26), 8313-8320 (2015);
doi:10.1021/acs.jpcb.5b04044

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