Experimental Biophysics @ Hurley Lab Theoretical Biophysics @ Hummer Lab
UC Berkeley Max Planck Institute of Biophysics
360 Stanley Hall Max von Laue Str. 3
Berkeley, CA 94720, USA 60438 Frankfurt am Main, Germany
joh.schoeneberg (at) berkeley.edu
We were giving a tutorial on our software and methods during the winter school 'Modeling Large Molecular Assemblies' in December 2014 in Nice.
ReaDDy is a particle-based reaction-diffusion simulation software. It features
One-week hands-on experiences to learn and develop in ReaDDy:
I did research different reaction-diffusion systems, including
The following picture provides an overview of applications and levels of modeling detail.
Figure 3: The figure shows three application examples of particle-based reaction-diffusion simulations. Left: Snapshots of a predator-prey simulation in the topology of the ReaDDy logo (full movie). Center: Simulation of synaptic exocytosis. Synaptic vesicles (yellow) can fuse with the membrane (grey disk) when thy bind a SNARE complex (red). SNARE complexes form from Syx (blue) and Snap-25 (grey) when they collide with a certain probability. Syx and Snap-25 are given attraction potentials and form clusters with themselves. A calcium channel is depicted (green) that emits Ca2+ ions (small green particles. Right: Fine-grain use of ReaDDy. The system depicted in Center in a finer molecular representation. Syx molecules consist of a membrane anchor (blue), an extended linker (red) and a terminal domain (dark gray). Synaptobrevin (orange+yellow) and synaptotagmin (dark green+grey+light green) are constructed in a similar way. Harmonic spring potentials provide the shape of the particle groups.
More movies here.
MHC class I molecules is depicted (blue). The peptide binding pocket is clearly visible (in between the two alpha-helices). A peptide that is bound to MHC is depicted in orange. B: Enhanced sampling results for peptide conformations within the MHC binding pocket (pocket is omitted form the visualization). The peptide backbone is depicted in cyan, the peptide side chains in red. Note the tighter binding on the termini of the peptide (left and right) and the higher degree of flexibility towards the center. C: Certain peptides have been found to occur in two distinct bound conformations (arginine residues (red) once sticking out (top) and once buried in the groove (bottom)). The sampling algorithm's performance is demonstrated by starting from one conformation (red eg. pointing upwards) and trying to sample the other (green eg. pointing down).
In order to decode the language of the immune system (to facilitate vaccine generation) , I did research on peptide binding to MHC class I proteins (stronger binding peptides correlate with a stronger immune response). I wrote a software that
1) determined peptide conformations in the binding pocket of MHC-class I proteins based on the MD substitute CONCOORD,
2) calculated the binding energy between peptide and binding pocket and
3) ranked different peptides according to their binding energy.
If sophisticated image analysis is required, I write ImageJ and Fiji Macros and Plugins to support my experimental collaborators.
The right hand side shows an image analysis application in which specific features in microscopy images were enhanced.
Figure 5: A sample of a microscopy image analysis is shown. Spots are to be selected that rapidly disappear by increasing in diameter. An algorithm was created that enhances these spots. The result of the enhancement is depicted on the right hand side.
2015 - today
Postdoc in experimental molecular membrane biochemistry and biophysics, Hurley Lab
Max Planck Institute of Biophysics
2014 - 2015
Postdoc in theoretical molecular membrane biochemistry and biophysics, Hummer Lab
Free University Berlin
2009 - 2014
Max Planck Institute for Molecular Genetics Berlin
2008 - 2009
Fast Track program for outstanding young researchers
2005 - 2008
Tiburtius PhD thesis price of the universities of Berlin (Anerkennungspreis), 2015
Marie Skłodowska-Curie postdoctoral fellowship, European Union, 2015
Poster Award, 4th International caesar Conference, Bonn, 2014
Steering committee member Junges Wissenschaftsforum Dahlem, FU-Berlin, 2013
2014, 8th Dec Practical on Molecular Structure Determination
2014, 28th Jul - 1st Aug ReaDDy Summer School 2014
2012, 26th Sep Workshop
Invited Talk 06/2014 McCammon Lab, San Diego, CA
Invited Talk 06/2014 Hurley Lab, San Diego, CA
Invited Talk 05/2014 Lipowsky Lab, Potsdam, Germany
Invited Talk 04/2014 Hummer Lab, Frankfurt, Germany
Poster 03/2014 4th International caesar Conference "Sensory Systems – from molecule to function", Bonn, Germany
Poster 03/2014 Membranes and Modules Conference 2014, Berlin, Germany
Invited Talk 02/2014 Dittrich Lab, Jena, Germany
Poster 10/2013 Macromolecular Crowding Effects in Cell Biology, Orléans, France
Contrib. Talk + ReaDDy Tutorial 10/2013 BDBDB3: Biological Diffusion and Brownian Dynamics Brainstorm 3, Heidelberg, Germany
Contrib. Talk 06/2013 European Meeting on Phototransduction, Delmenhorst, Germany
Contrib. Talk 04/2013 Computer Simulation and Theory of Macromolecules, Huenfeld, Germany
Contrib. Talk + ReaDDy Tutorial 10/2012 Cecam Workshop Signaling Pathways, Paris, France
Contrib. Talk 06/2012 International conference on molecular crowding, Askona, Switzerland
Poster 04/2012 Workshop Computer Simulation and Theory of Macromolecules, Huenfeld, Germany
Contrib. Talk 10/2010 BDBDB2: Biological Diffusion and Brownian Dynamics Brainstorm 2, Heidelberg, Germany
Poster 10/2010 Annual Meeting of the German Biophysical Society, Bochum, Germany
Poster 03/2010 Computer Simulation and Theory of Macromolecules, Huenfeld, Germany
Poster 10/2009 International Symposium Membranes and Modules, Berlin, Germany
Poster 05/2009 Molecular Kinetics, Berlin, Germany
Poster 10/2008 Interplay between Molecular Conformations and Biological Function, Bad Kissingen, Germany
M Gunkel*, J Schöneberg*, W Alkhaldi, S Irsen, F Noé, U B Kaupp, A Al-Amoudi, (2015) Higher-order architecture of rhodopsin in intact photoreceptors and its implication for phototransduction kinetics. Structure, 23(4): 628-38. (*equal contribution).
J Biedermann, A Ullrich, J Schöneberg and F Noé, (2015) ReaDDyMM: fast particle-based reaction-diffusion simulations using graphical processing units. Biophysical Journal, 108(3): 457-61.
J Schöneberg, A Ullrich, F Noé, (2014) Simulation tools for particle-based reaction-diffusion dynamics in continuous space. BMC Biophysics, 7(11).
J Schöneberg, M Heck, KP Hofmann, F Noé, (2014) Explicit Spatiotemporal Simulation of Receptor-G Protein Coupling in Rod Cell Disk Membranes. Biophysical Journal, 107(5): 1042-1053.
Y Posor, M Eichhorn-Gruenig*, D Puchkov*, J Schöneberg*, A Ullrich*, A Lampe, R Müller, S Zarbakhsh, F Gulluni, E Hirsch, M Krauss, C Schultz, J Schmoranzer, F Noé and V Haucke (2013) Spatiotemporal control of endocytosis by phosphatidylinositol-3,4-bisphosphate. Nature, 499 (7457): 233-237 (*equal contribution).
Welcome | ReaDDy | Reaction-Diffusion | Other Science | CV
I currently work in the Hurley and in the Hummer labs. At Berkeley, I'm engaged in BPEP. Before, in the Noé lab, I used to work in sfb740 and sfb958 projects. Download ReaDDy and collaborate with us on gitHub. Make sure to check out fraudinkel photography.