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.
Force probe simulations using an adaptive resolution scheme
Journal of Physics: Condensed Matter, (2021);
doi:10.1088/1361-648x/abed18
Supramolecular Packing Drives Morphological Transitions of Charged Surfactant Micelles
Angewandte Chemie International Edition59 (42),18591-18598 (2020);
doi:10.1002/anie.202004522
Force-dependent folding pathways in mechanically interlocked calixarene dimers via atomistic force quench simulations
Molecular Physics118 (19-20),e1743886 (2020);
doi:10.1080/00268976.2020.1743886
Mechanical and Structural Tuning of Reversible Hydrogen Bonding in Interlocked Calixarene Nanocapsules
The Journal of Physical Chemistry B123 (22),4688-4694 (2019);
doi:10.1021/acs.jpcb.9b02676
Temperature dependent mechanical unfolding of calixarene nanocapsules studied by molecular dynamics simulations
The Journal of Chemical Physics151 (4),045102 (2019);
doi:10.1063/1.5111717
Hybrid Particle-Field Molecular Dynamics Simulations of Charged Amphiphiles in an Aqueous Environment
Journal of Chemical Theory and Computation14 (9),4928-4937 (2018);
doi:10.1021/acs.jctc.8b00466
Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding
The Journal of Chemical Physics148 (4),044109 (2018);
doi:10.1063/1.5010435
Structural Origin of Metal Specificity in Isatin Hydrolase from Labrenzia aggregata Investigated by Computer Simulations
Chemistry - A European Journal24 (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
Biochemical and Biophysical Research Communications498 (2),327-333 (2018);
doi:10.1016/j.bbrc.2017.10.132
Force probe simulations using a hybrid scheme with virtual sites
The Journal of Chemical Physics147 (13),134909 (2017);
doi:10.1063/1.4986194
Force probe simulations of a reversibly rebinding system: Impact of pulling device stiffness
The Journal of Chemical Physics146 (12),124901 (2017);
doi:10.1063/1.4978678
Determining Factors for the Unfolding Pathway of Peptides, Peptoids, and Peptidic Foldamers
The Journal of Physical Chemistry B120 (40),10433-10441 (2016);
doi:10.1021/acs.jpcb.6b06784
Mechanical unfolding pathway of a model β-peptide foldamer
The Journal of Chemical Physics142 (20),204901 (2015);
doi:10.1063/1.4921371
Comparative Study of the Mechanical Unfolding Pathways of α- and β-Peptides
The Journal of Physical Chemistry B119 (26),8313-8320 (2015);
doi:10.1021/acs.jpcb.5b04044
Contact
- Prof. Dr.GregorDiezemann
- Institut für Physikalische Chemie
- Universität Mainz
- Duesbergweg 10-14
- D-55128Mainz
- Tel:+49 6131 39 23735
- diezemanHGHc_ACvWUE@xzFCuni-mainz.de
- https://www.tc.uni-mainz.de/gruppe-diezemann/
- Prof. Dr.JürgenGauß
- Institut für Physikalische Chemie
- Universität Mainz
- Duesbergweg 10-14
- D-55128Mainz
- Tel:+49 6131 39 23736
- gaussyuBImsGVq@YdKIcuni-mainz.de
- https://www.tc.uni-mainz.de/gruppe-gauss/