University of Stuttgart

Computational Biochemistry Group
(Kästner Group)
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Reviewed Publications:

Are Different Stoichiometries Feasible for Complexes Between Lymphotoxin-Alpha and Tumor Necrosis Factor Receptor 1
[26] “Are Different Stoichiometries Feasible for Complexes Between Lymphotoxin-Alpha and Tumor Necrosis Factor Receptor 1?” Nahren M. Mascarenhas and Johannes Kästner BMC Struct. Biol. in print (2012)
Deuterium Enrichment of Interstellar Methanol Explained by Atom Tunneling
[25] “Deuterium Enrichment of Interstellar Methanol Explained by Atom Tunneling” T. P. M. (Fedor) Goumans and Johannes Kästner J. Phys. Chem. A 115, 10767 (2011)
Kinetic Isotope Effects Calculated with the Instanton Method
[24] “Kinetic Isotope Effects Calculated with the Instanton Method” Jan Meisner, Judith B. Rommel and Johannes Kästner J. Comput. Chem. 32, 3456 (2011)
The Fragmentation–Recombination Mechanism of the Enzyme Glutamate Mutase Studied by QM/MM Simulations
[23] “The Fragmentation–Recombination Mechanism of the Enzyme Glutamate Mutase Studied by QM/MM Simulations” Judith B. Rommel and Johannes Kästner J. Am. Chem. Soc. 133, 10195 (2011)
Adaptive Integration Grids in Instanton Theory Improve the Numerical Accuracy at Low Temperature
[22] “Adaptive Integration Grids in Instanton Theory Improve the Numerical Accuracy at Low Temperature” Judith B. Rommel, Johannes Kästner J. Chem. Phys. 134, 184107 (2011)
Human Epidermal Growth Factor Receptor (EGFR) Aligned on the Plasma Membrane Adopts Key Features of Drosophila EGFR Asymmetry
[21] “Human Epidermal Growth Factor Receptor (EGFR) Aligned on the Plasma Membrane Adopts Key Features of Drosophila EGFR Asymmetry” Christopher J. Tynan, Selene K. Roberts, Daniel J. Rolfe, David T. Clarke, Hannes H. Loeffler, Johannes Kästner, Martyn D. Winn, Peter J. Parker, and Marisa Martin-Fernandez Mol. Cell. Biol. 31, 2241 (2011)
Cover page
Locating instantons in many degrees of freedom [20] “Locating Instantons in Many Degrees of Freedom” Judith B. Rommel, T. P. M. (Fedor) Goumans, Johannes Kästner, J. Chem. Theory Comput. 7, 690 (2011)
Umbrella Sampling
[19] “Umbrella Sampling” Johannes Kästner, Comput. Mol. Sci. 1, 932 (2011)
Hydrogen Atom Tunneling Could Contribute to H2 Formation in Space [18] “Hydrogen Atom Tunneling Could Contribute to H2 Formation in Space” T. P. M. Goumans, Johannes Kästner, Angew. Chem., Int. Ed. 49, 7350 (2010)
German version: “Tunneln von Wasserstoffatomen kann zur Bildung von H2 im Weltraum beitragen” Angew. Chem. 122, 7508 (2010)
cover page (German)
The ribosome catalyses peptide bond formation by providing high ionic strength [17] “The ribosome catalyses peptide bond formation by providing high ionic strength” Johannes Kästner, Paul Sherwood Mol. Phys. 108, 293 (2010)
DL-FIND: an Open-Source Geometry Optimizer for Atomistic Simulations [16] “DL-FIND: an Open-Source Geometry Optimizer for Atomistic Simulations” Johannes Kästner, Joanne M. Carr, Thomas W. Keal, Walter Thiel, Adrian Wander, Paul Sherwood J. Phys. Chem. A 113, 11856 (2009)
Free-energy surface of the alanine dipeptide obtained from two-dimensional umbrella integration [15] “Umbrella integration in two or more reaction coordinates” Johannes Kästner J. Chem. Phys. 131, 034109 (2009)
Reactive center of Fluorinase and the potential and free energy curves [14] “Finite-temperature effects in enzymatic reactions – Insights from QM/MM free-energy simulations” Hans Martin Senn, Johannes Kästner, Jürgen Breidung, Walter Thiel Can. J. Chem. 87, 1322 (2009)
EGFR ectodomain tetramer [13] “Ectodomain orientation, conformational plasticity and oligomerization of ErbB1 receptors investigated by molecular dynamics” Johannes Kästner, Hannes H. Loeffler, Selene K. Roberts, Marisa L. Martin-Fernandez, and Martyn D. Winn J. Struct. Biol. 167, 117 (2009)
nudged elastic band method [12] “An embedded cluster study of the formation of water on interstellar dust grains” T. P. M. Goumans, C. Richard A. Catlow, Wendy A. Brown, Johannes Kästner, and Paul Sherwood, Phys. Chem. Chem. Phys. 11, 5431 (2009)
Dimer Method [11] “Superlinearly converging dimer method for transition state search” Johannes Kästner, Paul Sherwood, J. Chem. Phys. 128, 014106 (2008)
Micro-iterative Optimization [10] “Exploiting QM/MM Capabilities in Geometry Optimization: a Microiterative Approach Using Electrostatic Embedding” Johannes Kästner, Stephan Thiel, Hans Martin Senn, Paul Sherwood, Walter Thiel, J. Chem. Theory Comput. 3, 1064 (2007)
Nitrogen Fixation [9] “Ammonia Production at the FeMo Cofactor of Nitrogenase: Results from Density Functional Theory” Johannes Kästner, Peter E. Blöchl, J. Am. Chem. Soc. 129, 2998 (2007)
Statistics in Umbrella Integration [8] “Analysis of the statistical error in umbrella sampling simulations by umbrella integration” Johannes Kästner, Walter Thiel, J. Chem. Phys. 124, 234106 (2006)
QM/MM Free-Energy Perturbation [7] “QM/MM Free-Energy Perturbation Compared to Thermodynamic Integration and Umbrella Sampling: Application to an Enzymatic Reaction” Johannes Kästner, Hans Martin Senn, Stephan Thiel, Nikolaj Otte, and Walter Thiel, J. Chem. Theory Comput. 2, 452 (2006)
Umbrella Integration [6] “Bridging the gap between thermodynamic integration and umbrella sampling provides a novel analysis method: Umbrella Integration” Johannes Kästner, Walter Thiel, J. Chem. Phys. 123, 144104 (2005)
Activation of Dinitrogen by Nitrogenase [5] “Activation and protonation of dinitrogen at the FeMo cofactor of nitrogenase” Johannes Kästner, Sascha Hemmen, and Peter E. Blöchl, J. Chem. Phys. 123, 074306 (2005). This paper in arXiv.org.
Acetylene Reduction by Nitrogenase [4] “Model for Acetylene Reduction by Nitrogenase Derived from Density Functional Theory” Johannes Kästner and Peter E. Blöchl, Inorg. Chem. 44, 4568 (2005)
Hydrogen addition to the FeMoco of Nitrogenase
[3] “Towards an Understanding of the Workings of Nitrogenase from DFT Calculations” Johannes Kästner and Peter E. Blöchl, ChemPhysChem 6, 1724 (2005)
FeMo-Cofactor of Nitrogenase
[2] “Nitrogen Binding to the FeMo-Cofactor of Nitrogenase” Johannes Schimpl, Helena M. Petrilli, and Peter E. Blöchl, J. Am. Chem. Soc. 125, 15772 (2003)
PAW wave functions
[1] “Projector augmented wave method: ab initio molecular dynamics with full wave functions” Peter E. Blöchl, Clemens J. Först, Johannes Schimpl, Bull. Mater. Sci. 26, 33 (2003)

Non-Reviewed Publications and Theses:

[11] “Durch Abkürzung schneller zum Ziel: Simulation des Tunneleffekts für große Moleküle” Johannes Kästner. Mediendienst Forschung, University of Stuttgart, 2011. (pdf)
[10] “QM/MM: Die Kombination aus Quantenmechanik und empirischen Kraftfeldern” Johannes Kästner. Trendbericht in the Nachrichten aus der Chemie, 2011. (pdf)
[9] “Excited State and Parallel Geometry Optimisation with DL-FIND” Thomas W. Keal, Joanne M. Carr, Adrian Wander, Paul Sherwood, Johannes Kästner. Chapter in “Frontiers 2009” – CSE Department's annual report for 2009.
[8] “Complex energy landscapes revealed: The phosphorylation reaction in protein kinase A” M. Montenegro, M. Garcia-Viloca, À. González-Lafont, J.M. Lluch, J. Kästner, J.M.H. Thomas, H.J.J. van Dam, and P. Sherwood. Chapter in “Frontiers 2008” – CSE Department's annual report for 2008.
[7] “Larger and longer: atomistic and coarse-grained simulations of the Epidermal Growth Factor Receptor” Hannes H. Loeffler, Johannes Kästner and Martyn D. Winn. Chapter in “Frontiers 2008” – CSE Department's annual report for 2008.
[6] “Finding Minima, Transition States, and Conical Intersections: the Development of a Geometry Optimiser for Atomistic Simulation Codes” Johannes Kästner and Paul Sherwood. Chapter in “Frontiers 2007” – CSE Department's annual report for 2007.
[5] “CSED Software to Leap Ahead” Adrian Wander, Paul Sherwood, William Smith, Coralia Cartis, Johannes Kästner, et al. Chapter in “Frontiers 2007” – CSE Department's annual report for 2007.
[4] “New Tools for the Accurate Study of Biomolecular Reactivity” Johannes Kästner, Paul Sherwood, Hans Martin Senn, Stephan Thiel, Nikolaj Otte, Walter Thiel. Chapter in “Frontiers 2006” – CSE Department's annual report for 2006.
[3] Book chapter “Electronic structure methods: Augmented Waves, Pseudopotentials and the Projector Augmented Wave method” Peter E. Blöchl, Johannes Kästner, Clemens J. Först, in “Handbook of Materials Modeling, Volume I (Methods and Models)” S. Yip Ed., Springer, ISBN: 1-4020-3287-0, May 2005
[2] Ph.D. thesis “Biological Nitrogen Fixation – Simulation of the Reaction Mechanism of Nitrogenase from First Principles” Johannes Kästner, Clausthal University of Technology (2004) pdf (6.7MB)
[1] Master thesis (diploma thesis) “Linkage Isomers of Transition Metal Nitrosyl Complexes studied by ab-initio Molecular Dynamics” Johannes Schimpl, Vienna University of Technology (2001)

Talks, Conference Contributions and Participations:

Presentations were given by J. Kästner unless notes otherwise

Invited Talks and Seminars

  1. University of Erlangen-Nürnberg, Computer-Chemie-Centrum, Atom Tunneling: from Astrochemistry to Enzymes, April 23, 2012
  2. University of Bonn, Chemistry Department, Multiskalensimulationen chemischer Reaktionsmechanismen, April 10, 2012
  3. TU Clausthal, Faculty of Natural and Materials Science, Germany: Atom Tunneling: from Astrochemistry to Enzymes, March 8, 2012
  4. TU Munich, Institute of Theoretical Chemistry, Germany: Exploiting QM/MM Capabilities in Geometry Optimization, Tunneling and Free-Energy Sampling, December 13, 2011
  5. University of Würzburg, Department of Chemistry and Pharmarcy, Germany: Multiscale Simulations of Chemical Reaction Dynamics, October 5, 2011
  6. Theoretical Chemistry group, Leiden Institute of Chemistry, Universiteit Leiden, Netherlands: Exploiting QM/MM Capabilities in Geometry Optimization and Free-Energy Sampling, September 20, 2011
  7. WATOC 2011, World Association of Theoretical and Computational Chemists, Santiago de Compostela, Spain: Accurate Tunneling Rates in Large Systems: Implications for Biochemical Reactions, July 17–22, 2011
  8. University of Vienna, Faculty of Chemistry, Austria: Multiscale Simulations of Biochemical Reaction Mechanisms, April 4, 2011
  9. Max-Planck-Institute for Solid State Research, Stuttgart, Germany: Unraveling biological nitrogen fixation: Insights from first-principles calculations, December 2, 2010
  10. Institute of Physical and Theoretical Chemistry, University of Würzburg, Germany: Exploiting QM/MM Capabilities in Geometry Optimization and Free-Energy Sampling, July 22, 2010
  11. University of St Andrews, School of Chemistry, UK: Tunnelling of Hydrogen Atoms Described by QM/MM Simulations: Implications for Biochemical Reactions, June 7, 2010
  12. HLN colloquium, University of Bochum, Germany: Biochemical Simulations using QM/MM Techniques, May 17, 2010
  13. Institute for Theoretical Chemistry, University of Marbrug, Germany: Unraveling biological nitrogen fixation: Insights from first-principles calculations, December 8, 2009
  14. Physical-chemical colloquium, University of Karlsruhe (TH), Germany: Biochemical Simulations using QM/MM Techniques, November 30, 2009
  15. Computational Molecular Biophysics Group, Heidelberg University, Germany: Orientation and oligomer topology of the ErbB1 receptor on the cell surface: a combined experimental / MD-simulation study, November 23, 2009
  16. TUD CSI Autumn School 2009 – “Molecular Simulations at Different Scales, Future and Perspectives on Modeling Interfaces”, TU Darmstadt, Germany: QM/MM - Introduction, and Applications of the QM/MM method, September 24 – 25, 2009
  17. The 238th ACS National Meeting, Washington, DC, USA: The workings of nitrogenase, August 16–20, 2009
  18. Third school of Quantum Chemistry ECQR2009, Rabat, Morocco: QM/MM methods in ChemShell, applied to biochemistry, June 3–6, 2009
  19. Theoretical Chemistry Colloquium, Center for Theoretical Chemistry, University of Bochum, Germany: Biochemical Simulations using QM/MM Techniques, May 20, 2009
  20. Graduate School (GRK 782) “Spectroscopy and Dynamics of Molecular Coils and Aggregates,” Göttingen, Germany: Orientation and oligomer topology of the ErbB1 receptor on the cell surface: a combined experimental / MD-simulation study, May 6, 2009
  21. 10th Teraflop Workshop, HLRS, Stuttgart, Germany: Biochemical Simulations using QM/MM Techniques, March 16–17, 2009
  22. Fritz-Haber-Institute, Berlin, Germany: QM/MM Calculations using ChemShell: Methodology and Applications, Dezember 10–12, 2008
  23. Collaborative Research Center on Selective Catalytic Oxidation of C–H Bonds with Molecular Oxygen, Stuttgart, Germany. Biochemical Simulations using QM/MM Techniques, November 19, 2008
  24. Gordon Research Conference on “Iron-Sulfur Enzymes,” Colby–Sawyer College, New London, NH, USA. Why is the FeMoco of nitrogenase so large? Insights from simulation, June 8–13, 2008
  25. 2nd CMM 'Users Meet Developers' Workshop on QM/MM Simulations, Philadelphia, PA, USA. ChemShell: a Modular QM/MM Simulation Package based on the Tcl Interpreter, August 24–26, 2007
  26. Invited talk at the Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany: Finding Minima and Transition States in Biological Systems using ChemShell, August 8, 2007
  27. Invited talk at Accelrys Software Inc., Cambridge, UK: QM/MM simulations of enzymatic reactions using ChemShell, June 28, 2007
  28. Computational Chemistry Codes Workshop, Daresbury Laboratory. Lecture: Dynamics and geometry optimization with ChemShell, April 11–13, 2007
  29. Workshop Methods of Molecular Simulation 2006, Interdisciplinary Center for Scientific Computing (IWR) Heidelberg, Germany. Invited talk: Umbrella integration: a novel analysis method for umbrella sampling simulations, September 20–22, 2006
  30. CECAM workshop State of the art, developments and perspectives of electronic structure calculations in the frame of the Projector Augmented-Wave (PAW) method., Lyon, France. Invited talk: Using PAW to break barriers: biological nitrogen fixation, June 13, 2006
  31. Scienomics seminar, Scienomics Inc., Paris. Invited talk: ChemShell – A general purpose QM/MM simulation tool, June 7, 2006
  32. Invited talk at the University of Düsselforf, Germany. In a Collaborative Research Center on Molecular Response to Electronic Excitation. Free Energies of Activation in Enzymatic Reactions, February 9, 2006
  33. Invited talk at Clausthal University of Technology, Germany. QM/MM free-energy simulations of enzymatic reactions, January 11, 2006
  34. Invited talk at Daresbury Laboratory, Warrington, UK. In silico biochemistry: from free-energy sampling to enzymatic mechanisms, September 29, 2005
  35. Invited talk at the Institute of Inorganic Chemistry, University of Würzburg, Germany. Unraveling biological nitrogen fixation: Insights from first–principles calculations, December 20, 2004
  36. Invited talk at the Max-Planck-Institut für biophysikalische Chemie, Göttingen, Germany. Unraveling biological nitrogen fixation: Insights from first–principles calculations, September 10, 2004
  37. Invited talk at the Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany. Unraveling biological nitrogen fixation: Insights from first–principles calculations, September 8, 2004
  38. Gordon Research Conference on “Electron Distribution & Chemical Bonding,” Mount Holyoke College, South Hadley, MA, USA. Invited talk: Unraveling biological nitrogen fixation: Insights from first–principles calculations, July 4–9, 2004
  39. Gordon Research Conference on “Nitrogen Fixation,” Colby–Sawyer College, New London, NH, USA. Invited talk: Active role of the FeMoco cage: a comprehensive model of the mechanism from first–principles calculations, June 20–25, 2004
  40. Invited talk at the Institute for Physical and Theoretical Chemistry, Bonn University, Germany. Reaction mechanism of the enzyme nitrogenase, December 11, 2003

Conference Contributions (Talks) and Institute Seminars

  1. DPG Spring Meeting, section AMOP, Stuttgart, Germany. Judith Rommel: Improvements to the Instanton Method: Tunneling in Large Systems, March 12–16, 2012
  2. MolMod2011, Heidelberg, Germany. Accurate Tunneling Rates for Large Systems: Implications for Biochemical Reactions, October 9–11, 2011
  3. 46th Symposium on Theoretical Chemistry, Münster, Germany. Judith Rommel: Tunneling Rates in the Enzyme Glutamate Mutase: the Instanton Method Applied to Large Systems, additional Poster by Johannes Kästner: Accurate Tunneling Rates Using the Instanton Approach: Implications for H2-formation in Space, September 26–30, 2010
  4. Gordon Research Conference on “Computational Chemistry,” Les Diablerets, Switzerland. Accurate Tunneling Rates in Large Systems: Implications for Biochemical Reactions, additional Poster by Judith Rommel: Accurate tunneling rates in coenzyme B12-dependent glutamate mutase, August 29 – September 3, 2010
  5. Söllerhaus-Seminar 2010, Mittelberg, Austria. Judith Rommel: Radical reactions catalyzed by adenosylcobalamin-dependent glutamate mutase, January 27–30, 2010
  6. 45th Symposium on Theoretical Chemistry, Neuss, Germany. How to find transition states in many thousand degrees of freedom? The dimer method improved for QM/MM simulations of enzymes, September 8–12, 2009
  7. Symposium on calculations of tunneling rates in large systems, Reykjavik, Iceland. DL-FIND, ChemShell, and the interface to Pandora, April 19, 2009
  8. Biomolecular Simulation 2008: frontiers of biomolecular simulation, Bristol, UK. DL-FIND: the development of a geometry optimiser for atomistic simulations, January 7–9, 2008
  9. Theory group seminar Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany. From Umbrella Sampling to Thermodynamic Integration, January 25, 2006
  10. Psi–K 2005 conference, Schwäbisch Gmünd, Germany. Contributed talk: Biological nitrogen fixation: insights from first–principles calculations, September 17–21, 2005
  11. 41st Symposium for Theoretical Chemistry, Innsbruck, Austria. Contributed talk: Nitrogenase: DFT Calculations Provide Insight into Biological Nitrogen Fixation, Poster: Bridging the gap between thermodynamic integration and umbrella sampling, September 5–7, 2005
  12. Theory group seminar Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany. Free-energy sampling on the DFT level: Free-Energy Perturbation, May 4, 2005
  13. HLRN–Workshop “Quantum chemistry/Density functional theory,” Berlin, Germany. Talk: PAW Rechnungen auf dem HLRN System und PC Clustern, July 8, 2003
  14. 17. Workshop on Novel Materials and Superconductors, Planneralm, Austria. Contributed talk: Non-Collinear Magnetism of Iron Sulfur Proteins, February 24 – March 2, 2002

Conference Contributions

  1. Psi–K 2010 conference, Berlin, Germany. Posters: Accurate Tunneling Rates using the Instanton approach: Implications for H2-formation in Space and The ribosome catalyses peptide-bond formation by providing high ionic strength, September 13–16, 2010
  2. First Principles Quantum Chemistry: from Elementary Reactions to Enzymes, Bad Herrenalb, Germany. Poster by Judith Rommel: Simulation of radical reactions with B12-dependent glutamate mutase, poster by Johannes Kästner: Finding Minima and Transition States in many Thousand Degrees of Freedom, April 14–17, 2010
  3. International Symposium on Theoretical and Computational Chemistry, Mülheim an der Ruhr, Germany. Poster by Judith Rommel: Simulation of radical reactions with B12-dependent glutamate mutase, poster by Johannes Kästner: Finding Minima and Transition States in many Thousand Degrees of Freedom, February 28 – March 2, 2010
  4. European Summer School for Quantum Chemistry (ESQC) 2009, Torre Normanna, Italy. Poster by Judith Rommel: Simulation of radical reactions with B12-dependent glutamate mutase, September 6–19 , 2009
  5. CMS 2008, Cirencester, UK. Poster: Finding Minima and Transition States in Biological Systems using ChemShell, June 22–25, 2008
  6. SimBioMa, Konstanz, Germany. Poster: Finding Minima and Transition States in Biological Systems using ChemShell, April 2–5, 2008
  7. Molecular Quantum Mechanics – Analytic Gradients and Beyond, Budapest, Hungary. Poster: Umbrella Integration in one or two Dimensions: Analysis of Umbrella-Sampling Simulations, May 29 – June 3, 2007
  8. BIOMOLECULAR SIMULATION 2007: faster, bigger, better, Nottingham, United Kingdom. Poster presentation: Umbrella integration: a novel analysis method for umbrella sampling simulations, January 3–5, 2007
  9. Gordon Research Conference on “Computational Chemistry,” Les Diablerets, Switzerland. Poster presentation: Umbrella integration: a novel analysis method for umbrella sampling simulations, October 8–13, 2006
  10. 19. Workshop on Novel Materials and Superconductors, Planneralm, Austria. Poster presentation: Unraveling biological nitrogen fixation: Insights from first–principles calculations, February 22–28, 2004
  11. “Workshop on Application of Density-Functional Theory in Condensed Matter Physics, Surface Physics, Chemistry, Engineering and Biology,” Fritz-Haber-Institut, Berlin, Germany. Poster presentation: Nitrogen Adsorption at the Cofactor of Nitrogenase, July 21–30, 2003
  12. Symposium “Computational Modelling of Catalysis,” Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany. Poster presentation: Nitrogen Adsorption at the Cofactor of Nitrogenase, July 16–18, 2003
  13. 18. Workshop on Novel Materials and Superconductors, Planneralm, Austria. February 23 – March 1, 2003
  14. 80th Bunsen Colloquium, Stuttgart, Germany. Main topic: computer simulations in physical chemistry: large molecules, liquids, solid state, May 24–26, 2001
  15. 16. Workshop on Novel Materials and Superconductors, Planneralm, Austria. Poster contribution: Molecular dynamics study of nitroprussides Na2[Fe(CN)5NO] used in holography, 2001
  16. Applied DFT2001: International Conference on Applied Density Functional Theory, Vienna, Austria, January 14–17, 2001
 
© 2003–12 · Impressum · last modified May 08, 2012