D7: Spatiotemporal simulation of module assembly and function

We are developing and applying efficient computational methods for the specific simulation requirements of functional modules. These methods rely on a combination of adaptive molecular dynamics simulations and particle-based reaction-diffusion simulations. We apply them to investigate the spatiotemporal mechanisms of rod cell phototransduction, initiated by Rhodopsin activation through light; and the scission of endocytosed vesicles mediated by Dynamin oligomerization and dynamics.

Selected Publications

Schöneberg J and Noé F
ReaDDy - a software for particle based reaction diffusion dynamics in crowded cellular environments.
PLoS ONE 2013; 8(9):e74261.
Faelber, K., Held, M., Gao, S., Posor, Y., Haucke, V., Noé, F., Daumke, O
Structural insights into dynamin-mediated membrane fission.
Structure 2012; 20(10):1621-1628.
Held M and Imhof P and Keller B and Noé F
Modulation of a ligand’s energy landscape and kinetics by the chemical environment.
J Phys Chem. B 2012; 46(116):13597-13607.
Peuker S, Cukkemane A, Held M, Noé F, Kaupp B, Seifert R
Kinetics of ligand-receptor interaction reveals an induced-fit mode of binding in a cyclic nucleotide-activated protein.
Biophys J 2012; 104:63-74.
Senne M., Trendelkamp-Schroer B., Mey ASJS., Schütte Ch. and Noé F
EMMA - A software package for Markov model building and analysis.
J Chem Theory Comput 2012; 8:2223-2238.
Posor Y, Eichhorn-Gruenig M, Puchkov D, Schöneberg J, Ullrich A, Lampe A, Müller R, Zarbakhsh S, Gulluni F, Hirsch E, Krauss M, Schultz C, Schmoranzer J, Noé F, Haucke V
Spatiotemporal control of endocytosis by phosphatidylinositol-3,4-bisphosphate.
Nature 2013; 499(7457):233-7.
Faelber, K., Posor, Y., Gao, S., Held, M., Roske, Y., Schulze, D., Haucke, V., Noé, F., Daumke, O.
Crystal structure of nucleotide-free dynamin.
Nature 2011; 477:556-60.
Splettstößer, T. and Holmes, K. C. and Noé, F. and Smith, J. C.
Structural modeling and molecular dynamics simulation of the actin filament.
Proteins 2011; 79:2033-2043.
Prinz, J.-H., Wu, H., Sarich, M., Keller, B., Senne M., Held, M., Chodera, J. D., Schütte, C., Noé, F.
Markov models of molecular kinetics: Generation and Validation.
J Chem Phys 2011; 134:174105.
Prinz, J.-H., Held, M., Smith, J. C., Noé, F.
Efficient Computation, Sensitivity and Error Analysis of Committor Probabilities for Complex Dynamical Processes.
Multiscale Model Simul 2011; 9:545-67.

Principal Investigator

Dr. Frank Noé

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