
D7 - Prof. Dr. Frank Noé
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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
- Authors:Trendelkamp-Schroer, B. and Wu, H. and Noé, F
Journal:arXiv Year:2016; :Pages:1603.01640.
Title:Reversible Markov chain estimation using convex-concave programming - Authors:Trendelkamp-Schroer, B. and Wu, H. and Noé, F
Journal:arXiv Year:2016; :Pages:1603.01640.
Title:Reversible Markov chain estimation using convex-concave programming - Authors:Scherer MK, Trendelkamp-Schroer B, Paul F, Pérez-Hernández G, Hoffmann M, Plattner N, Wehmeyer C, Prinz JH, Noé F
Journal:J Chem Theory Comput Year:2015; Volume:11Issue:(11):Pages:5525-42. doi: 10.1021/acs.jctc.5b00743. Epub 2015 Oct 14.
Title:PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models - Authors:Trendelkamp-Schroer B, Wu H, Paul F, Noé F
Journal:J Chem Phys Year:2015; Volume:143Issue:(17):Pages:174101. doi: 10.1063/1.4934536.
Title:Estimation and uncertainty of reversible Markov models - Authors:Ullrich, A. and Böhme, M. A. and Schöneberg, J. and Depner, H. and Sigrist, S. J. and Noé, F
Journal:PLoS Comput. Biol Year:2015; Volume:11Issue:(9):Pages:e1004407. doi: 10.1371/journal.pcbi.1004407. eCollection 2015 Sep.
Title:Dynamical organization of Syntaxin-1A at the presynaptic active zone - Authors:Gunkel M, Schöneberg J, Alkhaldi W, Irsen S, Noé F, Kaupp UB, Al-Amoudi A
Journal:Structure Year:2015; Volume:23Issue:(4):Pages:628-38. doi: 10.1016/j.str.2015.01.015. Epub 2015 Feb 26.
Title:Higher-order architecture of rhodopsin in intact photoreceptors and its implication for phototransduction kinetics - Authors:Hilsch, M., Goldenbogen, B., Sieben, C., Höfer, C.T., Rabe, J.P., Klipp, E., Herrmann, A., Chiantia, S
Journal:Biophys Year:2014; Volume:107Issue:(4):Pages:912-23. doi: 10.1016/j.bpj.2014.06.042.
Title:Influenza A matrix protein M1 multimerizes upon binding to lipid membranes - Authors:Wu, H. and Noé, F
Journal:SIAM Multiscale Model. Simul Year:2014; :Pages:12 . pp. 25-54.
Title:Optimal estimation of free energies and stationary densities from multiple biased simulations - Authors:Schöneberg, J. and Heck, M. and Hofmann, K. P. and Noé, F
Journal:Biophys J Year:2014; Volume:107Issue:(5):Pages:1042-1053. doi: 10.1016/j.bpj.2014.05.050.
Title:Explicit Spatio-temporal Simulation of Receptor-G Protein Coupling in Rod Cell Disk Membranes. - Authors:Schöneberg, J. and Ullrich, Alexander and Noé, F
Journal:BMC Biophys Year:2014; Volume:7Issue:(11):Pages:doi: 10.1186/s13628-014-0011-5. eCollection 2014.
Title:Simulation tools for particle-based reaction-diffusion dynamics in continuous space - Authors:Wu, H. and Mey, A.S.J.S. and Rosta, E. and Noé, F
Journal:J Chem Phys Year:2014; Volume:141Issue:(21):Pages:214106. doi: 10.1063/1.4902240.
Title:Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states - Authors:Schöneberg J and Noé F
Journal:PLoS ONE Year:2013; Volume:8Issue:(9):Pages:e74261.
Title:ReaDDy - a software for particle based reaction diffusion dynamics in crowded cellular environments - Authors: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
Journal:Nature Year:2013; Volume:499Issue:(7457):Pages:233-7.
Title:Spatiotemporal control of endocytosis by phosphatidylinositol-3,4-bisphosphate - Authors:Faelber, K., Held, M., Gao, S., Posor, Y., Haucke, V., Noé, F., Daumke, O
Journal:Structure Year:2012; Volume:20Issue:(10):Pages:1621-1628.
Title:Structural insights into dynamin-mediated membrane fission - Authors:Held M and Imhof P and Keller B and Noé F
Journal:J Phys Chem. B Year:2012; Volume:46Issue:(116):Pages:13597-13607.
Title:Modulation of a ligand's energy landscape and kinetics by the chemical environment - Authors:Peuker S, Cukkemane A, Held M, Noé F, Kaupp B, Seifert R
Journal:Biophys J Year:2012; Volume:104:Pages:63-74.
Title:Kinetics of ligand-receptor interaction reveals an induced-fit mode of binding in a cyclic nucleotide-activated protein - Authors:Senne M., Trendelkamp-Schroer B., Mey ASJS., Schütte Ch. and Noé F
Journal:J Chem Theory Comput Year:2012; Volume:8:Pages:2223-2238.
Title:EMMA - A software package for Markov model building and analysis - Authors:Faelber, K., Posor, Y., Gao, S., Held, M., Roske, Y., Schulze, D., Haucke, V., Noé, F., Daumke, O.
Journal:Nature Year:2011; Volume:477:Pages:556-60.
Title:Crystal structure of nucleotide-free dynamin - Authors:Splettstößer, T. and Holmes, K. C. and Noé, F. and Smith, J. C.
Journal:Proteins Year:2011; Volume:79:Pages:2033-2043.
Title:Structural modeling and molecular dynamics simulation of the actin filament - Authors:Prinz, J.-H., Wu, H., Sarich, M., Keller, B., Senne M., Held, M., Chodera, J. D., Schütte, C., Noé, F.
Journal: J Chem Phys Year:2011; Volume:134:Pages:174105.
Title:Markov models of molecular kinetics: Generation and Validation