Johannes Schöneberg

    Dr. Johannes Schöneberg, PhD

      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)

Welcome  |  FRET Structure Determination  |  ReaDDy  |  Reaction-Diffusion  |  CV


    I do theoretical, computational and experimental biophysics.

    Enjoy browsing my science!

smFRET-based Structure Determination of Intrinsically Flexible Proteins

Figure 1: As a first step in structure determination, an exhaustive ensemble of the conformation space is generated by molecular simulations. A: We start with a protein structure proposal that consists of a rigid domains (red, orange, grey) and flexible linkers (blue).  B: Coarse-grained replica exchange Monte Carlo simulations then explore the conformational space of the protein structure. This ensemble is the starting point for structure selection by using the experimentally derived smFRET distance distributions.

Tutorial on Software during Nice Winter School 2014

We were giving a tutorial on our software and methods during the winter school 'Modeling Large Molecular Assemblies' in December 2014 in Nice.


ReaDDy Logo Movie on Population Growth

ReaDDy is a particle-based reaction-diffusion simulation software. It features

  1. simulation in and on arbitrary geometries (i.e. 3D, 2D, spherical,...),
  2. spatial confinement (walls, boxes, tubes, ...),
  3. excluded volume of particles (crowding effects) and
  4. particle-particle interaction potentials (repulsion, attraction, clustering, ...).
ReaDDy's modular architecture separates between a 'particle dynamics'-core and a reaction engine. This allows to exchange the core by different dynamics implementations (there are currently a Brownian Dynamics and a Monte Carlo Core available) and third party particle codes. ReaDDy is open source under BSD-3clause. See more under, contribute under gitHub/readdy and read the paper under Schöneberg and Noé, PLOS ONE, 2013.
Figure 2: The ReaDDy logo and part of ReaDDy's software architecture is depicted. The architecture shows the feature of exchangeable paticle dynamics core implementations.

ReaDDy Summer Schools 

One-week hands-on experiences to learn and develop in ReaDDy:

Particle-Based Reaction-Diffusion Simulations

I did research different reaction-diffusion systems, including

  • The Rod cell photoactivation cascade
  • Ribosome-tRNA interaction
  • Synaptic Exocytosis
  • Synaptic Endocytosis
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.

Spatial Predator Prey Simulation

More movies here.

Constraint-Based Molecular Dynamics  /   Structure Prediction

Figure 4: MHC peptide structure prediction and enhanced sampling. A: An 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.

Scientific Image Analysis

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.


I take up new, exciting projects and solve challenging problems. I like to bridge between theory and  experiments to develop new theory and algorithms, apply them in calculations and simulations, verify them with experimental data and thereby guide both new experiments and theories.

UC Berkeley

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

PhD Biophysics
IMPRS PhD Student
Computational Molecular Biology, Prof. Frank Noé
Thesis: 'Reaction-diffusion dynamics in biologial systems - theory, computation, modeling and simulation. Application to the visual cascade and the synaptic vesicle cycle.'


MSc Bioinformatics
Completion in one year (instead of two as listed in the curriculum).
Thesis: 'Investigation of the reaction-diffusion processes of rod cell disc membrane photoactivation with single-particle resolution'
Advisor: Frank Noé

Max Planck Institute for Molecular Genetics Berlin

2008 - 2009

Fast Track program for outstanding young researchers
(Skip masters degree and advance to PhD with the BSc immediately. The Fast Track program included 1 year of courses before an exam would grant immediate advance to the PhD. I chose to do the 2 year MSc curriculum in that year. I successfully passed the Fast Track and additionally got the MSc.)

Saarland University

2005 - 2008

BSc Bioinformatics
Thesis: 'MHC:peptide structure prediction' with fast constraint based MD-Simulation substitute
Advisor: Rainer Böckmann

Awards and Honors 

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

Chosen student, Excellence Initiative Proposal , FU-Berlin, 2012

Best Poster Award, IMPRS-CBSC, MPI-Molgen Berlin 2009

IMPRS-CBSC fellowship for doctoral studies, MPI-Molgen Berlin, 2009

Fast Track fellowship, IMPRS-CBSC, MPI-Molgen Berlin, 2008

Konrad Adenauer fellowship for undergraduate studies, 2006

German Federal Cultural Foundation grant, 2006

Barmer Award for best high school diploma in biology, 2005

Scheffel Award for best high school diploma in German, 2005

Young Leaders Academy, 2004

Saarland Academy for highly gifted people, 2003

Organized Scientific Events

            2014, 8th Dec                         Practical on Molecular Structure Determination
                                                             During the winter school on 'Modeling Large Molecular Assemblies' in Nice
                                                             40 intnl. participants.


           2014, 28th Jul - 1st Aug         ReaDDy Summer School 2014
                                                             "Reaction Diffusion Dynamics in Biological Systems".
                                                             Lectures in the morning, practical sessions in the afternoon.
                                                             15 local, 5 intnl. participants.
                                                             topics: Diffusion, crowding, particle-based reaction-diffusion simulation, Monte Carlo sampling,
                                                             ReaDDy software

           2012, 26th Sep                       Workshop
                                                            "Simulation and modeling of signal transduction at cell membranes"
                                                            Lectures in the morning, practical session with the ReaDDy software in the afternoon.
                                                            13 local participants.

Scientific Contributions

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


> Pubmed      > Research Gate      > Google Scholar

J Schöneberg*, Lee IH*, Iwasa JH, Hurley JH, (2016) Reverse-topology membrane scission by the ESCRT proteinsNature Reviews Molecular Cell Biology, doi: 10.1038/nrm.2016.12. (*equal contribution).

Ullrich A, Böhme MA, Schöneberg J, Depner H, Sigrist SJ, Noé F, (2015) Dynamical Organization of Syntaxin-1A at the Presynaptic Active Zone. PLoS Comput Biology,11(9):e1004407.

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 kineticsStructure23(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 Journal108(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).

J Schöneberg, A Ullrich, Y Posor, V Haucke, F Noé (2013) Spatiotemporal model of a key step in endocytosis: SNX9 recruitment via phosphoinositides. arXiv:1307.4614.

J Schöneberg and F Noé (2013) ReaDDy - a software for particle based reaction diffusion dynamics in crowded cellular environments. PLOS ONE, 8 (9): e74261.

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.