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

Trendelkamp-Schroer, B. and Wu, H. and Noé, F
Reversible Markov chain estimation using convex-concave programming.
arXiv 2016; :1603.01640.
Trendelkamp-Schroer, B. and Wu, H. and Noé, F
Reversible Markov chain estimation using convex-concave programming.
arXiv 2016; :1603.01640.
Scherer MK, Trendelkamp-Schroer B, Paul F, Pérez-Hernández G, Hoffmann M, Plattner N, Wehmeyer C, Prinz JH, Noé F
PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models.
J Chem Theory Comput 2015; 11(11):5525-42. doi: 10.1021/acs.jctc.5b00743. Epub 2015 Oct 14.
Trendelkamp-Schroer B, Wu H, Paul F, Noé F
Estimation and uncertainty of reversible Markov models.
J Chem Phys 2015; 143(17):174101. doi: 10.1063/1.4934536.
Ullrich, A. and Böhme, M. A. and Schöneberg, J. and Depner, H. and Sigrist, S. J. and Noé, F
Dynamical organization of Syntaxin-1A at the presynaptic active zone.
PLoS Comput. Biol 2015; 11(9):e1004407. doi: 10.1371/journal.pcbi.1004407. eCollection 2015 Sep.
Gunkel M, Schöneberg J, Alkhaldi W, Irsen S, Noé F, Kaupp UB, Al-Amoudi A
Higher-order architecture of rhodopsin in intact photoreceptors and its implication for phototransduction kinetics.
Structure 2015; 23(4):628-38. doi: 10.1016/j.str.2015.01.015. Epub 2015 Feb 26.
Hilsch, M., Goldenbogen, B., Sieben, C., Höfer, C.T., Rabe, J.P., Klipp, E., Herrmann, A., Chiantia, S
Influenza A matrix protein M1 multimerizes upon binding to lipid membranes.
Biophys 2014; 107(4):912-23. doi: 10.1016/j.bpj.2014.06.042.
Wu, H. and Noé, F
Optimal estimation of free energies and stationary densities from multiple biased simulations.
SIAM Multiscale Model. Simul 2014; :12 . pp. 25-54.
Schöneberg, J. and Heck, M. and Hofmann, K. P. and Noé, F
Explicit Spatio-temporal Simulation of Receptor-G Protein Coupling in Rod Cell Disk Membranes..
Biophys J 2014; 107(5):1042-1053. doi: 10.1016/j.bpj.2014.05.050.
Schöneberg, J. and Ullrich, Alexander and Noé, F
Simulation tools for particle-based reaction-diffusion dynamics in continuous space.
BMC Biophys 2014; 7(11):doi: 10.1186/s13628-014-0011-5. eCollection 2014.
Wu, H. and Mey, A.S.J.S. and Rosta, E. and Noé, F
Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states.
J Chem Phys 2014; 141(21):214106. doi: 10.1063/1.4902240.
Schöneberg J and Noé F
ReaDDy - a software for particle based reaction diffusion dynamics in crowded cellular environments.
PLoS ONE 2013; 8(9):e74261.
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., 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.
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.

Principal Investigator

Dr. Frank Noé

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