Current Position
Berkeley Experimental Biophysics
360 Stanley Hall, Berkeley 94720, USA
Research
Dissertation
- Submitted July 2014
- Reaction-Diffusion Dynamics in Biological Systems
Research Interests
- Particle Dynamics Simulation
- Brownian Dynamics
- Reaction Diffusion Kinetics
- Computational Immunology
- Synthetic Biology
Education
- Scholarships
- 2008 - 2009: Stipend in the preparatory program of the IMPRS-CBSC
- 2006 - 2008: Undergraduate scholarship from the Konrad-Adenauer-Stiftung e.V.
- Advanced trainings
-
08-10 Dec 2012, GPU-programming course "CUDA" at HLRS, Stuttgart, Germany
- 06-14 July 2009, Molecular Simulation, CCP5 Summer School, Sheffield University, UK
- University
- 2008-2014 Free University of Berlin (FU Berlin)
- 2005-2008 Saarland University of Saarbrücken
- Degrees
- M.Sc (Bioinformatics, Dec. 2010), FU Berlin
- B.Sc (Bioinformatics, Jan. 2009), Saarland University
- Projects/Research
- 2010 Subproject D7 funded in the second funding period of SFB 740: "From molecular patterns to transport in specific geometries: Spatial effects on the function of the phototransduction module"
- 2009 Modeling of the primary rod vision signal transduction pathway on the disc membrane by using particle dynamics simulations, CMB Group, Free University of Berlin; supervised by Dr. Frank Noé
- 2008 Prediction of MHC:peptide structure ensembles by using conformation sampling and free energy computation, TComB Group, Saarland University; supervised by Dr. Rainer Boeckmann
- Conferences/Workshops
- June 2013; Conference "European Meeting on Phototransduction", Delmenhorst, Germany; oral presentation
- April 2013; Workshop "Computer Simulation and Theory of Macromolecules", Huenfeld, Germany; oral presentation
- Oct 2012; Cecam Workshop "Signaling Pathways", Paris, France, contributed talk, 2.5h oral software tutorial
- Sept 2012; Conference "Biomembrane Days in Potsdam", Potsdam , Germany; poster presentation
- Jun 2012; Conference "International conference on Molecular Crowding 2012", Ascona, Switzerland; contributed talk
- Apr 2012; Workshop "Computer Simulation and Theory of Macromolecules", Huenfeld, Germany; poster presentation
- Oct 2010; BDBDB2: "Biological Diffusion and Brownian Dynamics Brainstorm 2", Heidelberg, Germany
- Oct 2010; "Annual Meeting of the German Biophysical Society", Bochum, Germany
-
Mar 2010; Workshop "Computer Simulation and Theory of Macromolecules", Huenfeld, Germany
- Dec 2009; International Symposium "Membranes and Modules", FU Berlin
- May 2009; Molecular Kinetics Workshop 2009; Institute of Mathematics and Informatics, Free University of Berlin
- Nov 2008; Oberwolfach-Seminar: "Applied Time Series Analysis in Scientific Computing"; Mathematisches Forschungsinstitut Oberwolfach
Publications from time as IMPRS fellow
- M Gunkel*, J Schöneberg*, W Alkhaldi, S Irsen, F Noé, UB Kaupp, A Al-Amoudi (2015) Higher-order architecture of rhodopsin in intact photoreceptors and its implication for phototransduction kinetics. Structure, 23 (4): 628-38
- J Biedermann, A Ullrich, J Schöneberg, F Noé (2015) ReaDDyMM: Fast interacting particle reaction-diffusion simulations using graphical processing units. Biophys J., 108 (3): 457-61
- J Schöneberg, M Heck, KP Hofmann, F Noé (2014) Explicit spatiotemporal simulation of receptor-g protein coupling in rod cell disk membranes. Biophys J., 107 (5): 1042-53
- J Schöneberg and F Noé (2013) ReaDDy - a software for particle based reaction diffusion dynamics in crowded cellular environments. PLOS One, 8 (9): e74261
- 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 [q-bio.BM].
- Y Posor et al. (2013)
Spatiotemporal control of endocytosis by phosphatidylinositol-3,4-bisphosphate.
Nature, 499 (7457): 233-237 - J Seibert (2010)
Investigation of the reaction-diffusion processes of rod cell disc membrane photoactivation with single-particle resolutioM.Sc thesis at the FU Berlin, 2010, supervised by Dr. Frank Noé and Prof. Dr. Christof Schütte - J Seibert (2008)
MHC:peptide Structure Prediction.
B.Sc thesis at Saarland University Saarbrücken, 2008, supervised by Dr. Rainer Boeckmann and Prof. Dr. Hans-Peter Lenhof
* joint first authors