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Achievements

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Here is a list of all our achievements.

Peer-Reviewed Papers

In Preparation

  • M. Hülsmann, C.M. Friedrich, D. Reith: 2nd paper - German Automobile Market.
  • Farag F Selim; Anke C Schiedel; Astrid Maaß; Christa E Müller: -- 2.pub im Rahmen der Doktorarbeit von Farag
  • P. Simeon, D. Reith, T. Soddemann, A. Arnold. A CUDA implementation of the Gram-Schmidt method. (in preparation)
  • T. Köddermann, A. Arnold, D. Reith: “Partition Coefficients of diverse ionic liquids by means of free energy calcucations” (in preparation)
  • T. Köddermann, U. Kragl, R. Ludwig: On the electrical conductivity of [Cn MIM][NTf2]: A molecular dynamics study. in preparation for Angew.Chemie
  • T. Köddermann, R. Ludwig: Force field development for Ionic Liquids I: A united atom force field for [CnMIM][NTf2]. in preparation
  • T. Köddermann, R. Ludwig: Force field development for Ionic Liquids II: A united atom force field for [CnMIM][EtSO4]. in preparation
  • T. Köddermann, P. Schulz, R. Ludwig: Pressure behaviour and IL/water mixture properties of [C2MIM][EtSO4]. in preparation
  • Kirschner , K.N. and Arndt, H.-D. “Dynamics of the Ribosomal L11·23S Complex with a Bound Thiopeptide Antibiotic.” Manuscript is in preparation.
  • Arndt, H.-D., Baumann, S., Hiller, F., Jonker, H.R.A., Kirschner, K.N., Wolf, A. Schoof, S. and Schwalbe, H., “Thiostrepton NMR structures reveal shape selectivity in target recognition.” Manuscript is in preparation.
  • Baumann, S., Kirschner, K.N. and Arndt, H.-D., “Characterization of the Thiopeptide Binding Site on E. coli 70S Ribosomes by Proximity Induced Covalent Capture (PICC).” Manuscript is in preparation.
  • Schoof, S., Aminake, M.N., Pradel, G., Ellinger, B., Baumann, S., Potowski, M., Najajreh, Y., Kirschner, K.N. and Arndt, H.-D., “Anti-plamodial Thiostrepton Derivatives Inhibit the Proteasome's Caspase-like Activity.” Manuscript is in preparation.
  • Bittracher, A., Junge, O. Reith, D. Kirschner, K.N., “Properties of a PMMA Triad” Manuscript is in preparation.
  • Karimi, H.A., Kirschner, K.N., Algear, E., Müller-Plathe, F., Reith, D. “Structural and Dynamical Properties of PMMA by means of multiscale simulations” Manuscript is in preparation.
  • Kirschner , K.N. “ExTrM Force Field: Saturated and Simple Unsaturated Esters and Aldehydes.” Submitted to Journal of Compuatational Chemistry.


Submitted


  • A. Maaß, E.D. Tekin, A. Schüller, A. N. Palazoglu, D. Reith, R. Faller. „Comparing the Folding and Unfolding Characteristics of Short Peptides using Principal Component Analysis” Submitted to BBA – Proteins and Proteomics
  • M. Hülsmann, T.J. Müller, T. Köddermann, D. Reith: “Automated Force Field Optimisation of Small Molecules using a Gradient–Based Workflow Package.” Submitted to Molecular Simulation
  • N. Gribova, A. Arnold, H. Maleki, T. Schilling, C. Holm. “2D versus 3D Freezing of a Lennard-Jones Fluid in a Slit Pore: A Molecular Dynamics Study.” Submitted to J. Chem. Phys.
  • A. Arnold, “On the calculation of the dielectric constant in computer simulations of ionic systems.” Submitted to J. Chem. Phys.


Accepted

  • Maaß, A., Nikitina, L., Clees, T., Kirschner, K.N., and Reith, D.: “Multi-objective force field optimization on basis of random models for ethylene oxide” to appear in Molecular Simulations. (2010)
  • Kirschner, K.N., Heikamp, K., and Reith, D.: “Atomistic Simulations of Isotactic Poly(Methyl Methacrylate) Melts: Exploring the Backbone Conformation.” to appear in Molecular Simulations. (2010)


2010

  • M. Hülsmann, J. Vrabec, A. Maaß, D. Reith: “Assessment of Numerical Optimization Algorithms for the Development of New Molecular Models” Comp. Phys. Comm. 181 (2010) 887–905, http://dx.doi.org/10.1016/j.cpc.2010.01.001
  • M. Hülsmann, T. Köddermann, J. Vrabec, D. Reith: GROW: A Gradient-based optimization workflow for the automated development of molecular models, Comp. Phys. Comm. 181 (2010) 499–513, http://dx.doi.org/10.1016/j.cpc.2009.10.024


2009

  • Farag F Selim; Anke C Schiedel; Astrid Maaß; Christa E Müller. Homology modelling of the human adenosine A2B receptor based on bovine rhodopsin and the ß2-adrenergic receptor: comparison of the binding modes obtained for agonists and antagonists" Journal of Computer-Aided Molecular Design . (2009) 23:807
  • V. Ballenegger, A. Arnold, J. J. Cerda. Simulations of non-neutral slab systems with long-range electrostatic interactions in 2D periodic boundary conditions, J. Chem. Phys. 131:094107 (2009).
  • Brühl, Bernhard; Hülsmann, Marco; Borscheid, Detlef; Friedrich, Christoph M.; Reith, Dirk: A Sales Forecast Model for the German Automobile Market Based on Time Series Analysis and Data Mining Methods. In: Perner, Petra (Hrsg.): Advances in data mining : applications and theoretical aspects. Berlin: Springer, 2009, S. 146-160 (Lecture notes in computer science 5633 : Lecture notes in artificial intelligence).http://dx.doi.org/10.1007/978-3-642-03067-3%5F13
  • T. Köddermann, K. Fumino, R. Ludwig, J. N. C. Lopes, A. A. H. Pádua: What far-infrared spectra can contribute to the development of force fields used in molecular dynamics simulations. Chem. Phys. Chem., 10: 1181-1186, 2009. http://dx.doi.org/10.1002/cphc.200900144
  • Kasam, Vinod; Salzemann, Jean; Botha, Marli; Dacosta, Ana; Degliesposti, Gianluca,; Isea, Raul; Kim, Doman; Maaß, Astrid; Kenyon, Colin; Rastelli, Giulio; Hofmann-Apitius, Martin; Breton, Vincent: WISDOM-II: Screening against multiple targets implicated in malaria using computational grid infrastructures, Malaria Journal 2009, 8, 88. http://dx.doi.org/10.1186/1475-2875-8-88
  • Maaß, Astrid; Müller, T.J.; Nikitina, Lialia; Hülsmann, Marco. The perfect fit? : Balancing predictive power and computational complexity for an atomistic model as prerequisite for nano-scale simulations. Chemistry central journal 3 (2009), Supplement 1. http://dx.doi.org/10.1186/1752-153X-3-S1-O14
  • Joseph, L.C., Bennett, J. A., Kirschner, K. N. , Shields, G.C. Hughes, Lostritto, N., J. Jacobson, H. I. and Andersen, T. T., “Antiestrogenic and Anticancer Activities of Peptides Derived from the Active Site of Alpha-Fetoprotein.” J. Pept. Sci 15 (2009) 319.
  • Salisburg, A.M., Deline A. L., Lexa, K.W., Shields, G.C., and Kirschner, K.N., “Ramachandran-type Plots for Glycosidic Linkages: Examples from Molecular Dynamic Simulations using the Glycam06 Force Field.” Journal of Computational Chemistry 30: 910–921, 2009.


2008

  • S. Tyagi, A. Arnold and C. Holm. Electrostatic layer correction with image charges: A linear scaling method to treat slab 2D+h systems with dielectric interfaces. J. Chem. Phys. 129:204102 (2008).
  • A. Arnold and C. Holm. Interactions of like-charged rods at low temperatures: Analytical theory vs. simulations. Euro. Phys. J. E, DOI:10.1140/epje/i2007-10347-4, 2008.
  • J. A. van Meel, A. Arnold, D. Frenkel, S. F. Portegies Zwart and R. G. Belleman. Harvesting graphics power for MD simulations. Molecular Simulation 34(3):259-266, 2008.
  • Scholz, Joachim; Toska, Karen; Luborzewski, Alexander; Maaß, Astrid; Schünemann, Volker; Haavik, Jan; Moser, Andreas: Endogenous tetrahydroisoquinolines associated with Parkinson's disease mimic the feedback inhibition of tyrosine hydroxylase by catecholamines, FEBS Journal 2008, 275 (9) 2109-2121.
  • Müller, Thomas J; Roy, Sudip; Zhao, Wei; Maaß, A; Reith, D: Economic simplex optimization for broad range property prediction: Strengths and weaknesses of an automated approach for tailoring of parameters, Fluid Phase Equilibria 2008, 274 (1-2), 27-35. DOI: 10.1016/j.fluid.2008.06.009
  • T. Köddermann, D. Paschek, R. Ludwig: On the Validity of Stokes-Einstein and Stokes-Einstein-Debye Relations in Ionic Liquids and Ionic Liquids Mixtures. ChemPhysChem, 9: 1851-1858, 2008.
  • D. Paschek, T. Köddermann, R. Ludwig: The Solvophobic Solvation and Interaction of Small Apolar Particles in Imidazolium-Based Ionic Liquids is Characterized by Enthalpy-/Entropy-Compensation. Phys. Rev. Lett., 100: 115901, 2008.
  • T. Köddermann, D. Paschek, R. Ludwig: Ionic Liquids: Dissecting the Enthalpies of Vaporization. ChemPhysChem, 9: 549-555, 2008.
  • Sherer, E.C., Kirschner, K.N., Pickard IV, F.C., Rein, C., Feldgus, S., and Shields, G.C., “Efficient and Accurate Characterization of the Bergman Cyclization for Several Enediynes Including an Expanded Substructure of Esperamicin A1.” Journal of Physical Chemistry B, 112, 16917-16937 (2008).
  • Allodi, M.A.; Kirschner, Karl N.; Shields, George C.:Thermodynamics of the hydroxyl radical with isoprene.In: The journal of physical chemistry / A, Molecules, spectroscopy, kinetics, environment & general theory 112 (2008), 30, S. 7064-7071 http://dx.doi.org/10.1021/jp801869c
  • Hartt, Gregory M.; Shields, George C.; Kirschner, Karl N.:Atmospheric OCS with one to four water molecules. In: The journal of physical chemistry / A, Molecules, spectroscopy, kinetics, environment & general theory 112 (2008), 19, S. 4490-4495 http://dx.doi.org/10.1021/jp800229k
  • Kirschner, K. N.; Yongye A.B., Tschampel S.M., Daniels C.R., Foley, B.L. and Woods, R.J., “GLYCAM06: a generalizable biomolecular force field. Carbohydrates.” In: Journal of Computational Chemistry 29 (2008), 4, S. 622-655.
  • Jacq, Nicolas; Salzemann, Jean; Legré, Yannick; Medernach, Emmanuel; Montagnat, Johan; Maaß, Astrid; Reichstadt, Matthieu; Schwichtenberg, Horst; Sridhar, Mahendrakar; Kasam, Vinod; Zimmermann, Marc; Hofmann, M.; Breton, Vincent:Grid-enabled virtual screening against malaria.In: Journal of grid computing 6 (2008), 1, S. 29-43 http://dx.doi.org/10.1007/s10723-007-9085-5
  • Jambor, Ramon; Kasná, Blanka; Kirschner, Karl N.; Schürmann, Markus; Jurkschat, Klaus:[{2,6-(Me2NCH2)2C6H3}Sn]2 : an intramolecularly coordinated diorganodistannyne.In: Angewandte Chemie 47 (2008), 8, S. 1650-1653 http:dx.doi.org/10.1002/anie.200704635


2007

  • V.A. Harmandaris, D. Reith, N.F.A. van der Vegt, and K. Kremer: “Comparison Between Coarse-Graining Models for Polymer Systems: Two Mapping Schemes for Polystyrene”, Macromol. Chem. Phys. 208, 2109-2120, 2007. DOI: 10.1002/macp.200700245
  • Jacq, Nicolas; (…); Maaß, Astrid; (…):Grid-Enabled High Throughput Virtual Screening.In: Dubitzky, Werner (Hrsg.) u.a.:Distributed, high-performance and Grid computing in computational biology : international workshop, GCCB 2006, Eilat, Israel, January 2007.Berlin [u.a.] : Springer, 2007, S. 45-59 (Lecture notes in computer science 4360 : Lecture notes in bioinformatics). http://dx.doi.org/10.1007/978-3-540-69968-2%5F5
  • Kasam, Vinod; Zimmermann, Marc; Maaß, Astrid; Schwichtenberg, Horst; Wolf, Antje; Jacq, Nicolas; Breton, Vincent; Hofmann-Apitius, Martin: Design of New Plasmepsin Inhibitors : a Virtual High Throughput Screening Approach on the EGEE Grid.In: Journal of chemical information and modeling 47 (2007), 5, S. 1818-1828 http://dx.doi.org/10.1021/ci600451t
  • Marco Hülsmann and Christoph M. Friedrich: "Comparison of a Novel Combined ECOC Strategy with Different Multiclass Algorithms Together with Parameter Optimization Methods", In: Perner, Petra (Hrsg.): Proceedings of the 5th international conference on Machine Learning and Data Mining in Pattern Recognition (Leipzig, Germany). Berlin/Heidelberg: Springer, 2007, S. 17-31 (Lecture notes in artificial intelligence 4571). http://dx.doi.org/10.1007/978-3-540-73499-4_3


Posters

  • Astrid Maaß et al.: “WISDOM 2 – Docking and MD on the Grid”, Gromacs Workshop 2007, Helsinki, February 2007
  • Dirk Reith et al.: “Structural and Dynamical Properties of Polystyrene determined by Coarse-Graining MD Simulations”, „NanoscaleS“-Conference, Salerno, Italy, July 2007
  • Astrid Maaß et al.: “Computation of thermodynamical properties by molecular simulation after automated force field optimization” European polymer congress 2007, Portoroz, July 2007
  • Dirk Reith et al.: “Structural and Dynamical Properties of Polystyrene determined by Coarse-Graining MD Simulations” SOCOBIM-Conference (Satelite to StatPhys-23), Citta del Mare, Sicily, Italy, September 2007
  • Astrid Maaß et al.: “Tailoring of parameters for broad range property predictions by simplex optimization and interactive design parameter optimization” , Liquids-Conference 2008, Lund, June 2008
  • A. Arnold et al.: “ESPResSo++ - An Extensible Simulation Package for Research on Soft Matter” April 2008, SimBioMa conference, Konstanz, Germany November 2008, Jülich soft matter days, Bonn, Germany March 2009, DPG Frühjahrstagung, Dresden, Germany
  • Marco Hülsmann et al.: “Enhancing Automated Parameter Optimization for the Computation of Thermodynamical Properties by Molecular Simulation”, Summer School TU Darmstadt, September 2008.
  • Farag F. Sherbiny et al.: German Conference on Chemoinformatics, Goslar, November 2008
  • Thorsten Köddermann et al.: "Automatically Parameterised and Reliable MD Force Fields for Ionic Liquids", DFG-SPP1191 Program Progress Meeting. Bamberg, March 2009
  • Antje Wolf et al.: “Toward modelling strategies for RNA-protein drug targets: a case study on the bacterial ribosome”, VII European Workshop in Drug Design, Siena, Italy, May 2009
  • Farag F. Sherbiny et al.:, Italian conference (Third Joint Italian-German Purine Club Meeting 'Purinergic Receptors: New Frontiers for Novel Therapies'), Camerino, Italy, July 2009.
  • Astrid Maaß et al.: “Modelling beyond manual intervention -- Approach routes to a most useful molecular description”, FOMMS-Conference 2009, Semiahmoo (Blaine), USA, July 2009
  • Karl N. Kirschner et al.: “Towards Developing Mesoscale Models for Organic and Bioorganic Polymers. A Case Study on PMMA and Carbohydrate Polymers”, FOMMS-Conference 2009, Semiahmoo (Blaine), USA, July 2009
  • Jon Halversson et al.: “Soft Matter Research and the Novel Features of the ESPResSo++ Simulation Package”, FOMMS-Conference 2009, Semiahmoo (Blaine), USA, July 2009
  • Thorsten Köddermann et al.: "Molecular Dynamics Simulation: A Powerfull Tool for Engineering Condenest Matter", EUCHEM, Bamberg, Germany, March 2010
  • Marco Hülsmann et al.: "GROW: A Gradient-based Optimization Workflow for Model Building beyond Manual Intervention", ProcessNet Working Party Molecular Modeling and Simulation for Process and Product Design, Würzburg, Germany, March 2010

Talks

  • Dirk Reith: “Mesoscale Coarse-Graining - A reliable route to enhance simulations” Invited Talk. Group Seminar College of Engineering, Koc Universität, Istanbul, Turkey, Februar 2007
  • Dirk Reith: “Mesoscale Coarse-Graining - Approaches and Results” Invited Talk. Group Seminar School of Chem. Engineering, National Technical University of Athens, Greece, May 2007
  • Marco Hülsmann: „A novel Combined ECOC Strategy for Multiclass Learning together with Parameter Optimization Methods“, 5th International Conference on Machine Learning and Data Mining (MLDM) 2007, Leipzig, Germany, July 2007
  • Dirk Reith: “Computersimulationen in der Chemie – Eine andere Art von Experiment“ Invited Talk. Public Seminar of the Rhein-Ahr-Campus, Remagen, Germany, July 2007
  • Dirk Reith: “Mesoscale Coarse Graining - Methods and Results for various polymer” Contributed Talk. „NanoscaleS“ - Conference Salerno, Italy September 2007
  • Astrid Maaß et al.: “Property prediction and multiscale modeling in drug research and polymer science”, CADFEM-Tagung Dresden, November 2007
  • Dirk Reith: “Automatic tailoring of parameters for robust and broad range property predictions by simplex optimization” Contributed Talk “AIChE Annual Meeting 2007“, Salt Lake City, UT, USA November 2007
  • Anton Schüller: "Große Gleichungssysteme und Anwendungen - Erfahrungen mit Mathe-Workshops für Hochbegabte", Workshop „Anwendungsorientierung im Mathematikunterricht am Gymnasium“, Köln, Dezember 2007
  • A. Arnold: “Segregation of flexible polymers in confinement”, Invited talk, Complex Fluids and Biology seminar, University of Leiden, The Netherlands, February 2008
  • A. Arnold and J. van Meel: “GPGPU - General Purpose Graphics Processing Unit”, Invited talk, University of Mainz, Germany, May 2008
  • Marco Hülsmann: „Parameter Optimization and Data Mining in Molecular Simulations“, Summer School Hall in Tirol, August 2008.
  • Dirk Reith: “Structural and Dynamical Properties of Polystyrene determined by Mesoscale MD Simulations” Contributed Talk „AIChE Annual Meeting 2008“, Philadelphia, PA, USA, November 2008
  • Anton Schüller: "Mathematik für die Praxis", Invited Talk, Woche der Mathematik, Amos-Comenius-Gymnasium, Bonn, November 2008
  • Astrid Maaß: “The perfect fit? Balancing predictive power and computational complexity for an atomistic model as prerequisite for nano-scale simulations”, Contributed Talk, GCC Goslar, November 2008
  • A. Arnold: “Electrostatics in ESPResSo”, Invited talk, Institut für Computerphysik, University of Stuttgart, Germany, March 2009
  • Anton Schüller: "Algorithmische Mathematik für die Schule - Erfahrungen und Ansätze", Kongress "Mathematik in der Praxis“, Berlin, March 2009
  • A. Arnold: “ESPResSo++ - Extensible Simulation Package for Research on Soft Matter”, CECAM workshop on heterogeneous nucleation, Zürich, Switzerland, April 2009
  • A. Arnold: “Electrostatics in ESPResSo”, ETH Zürich, Switzerland, April 2009
  • Dirk Reith: “Moderne Verfahren der Materialsimulation – Wie kommt man zur robusten Anwendung?” Invited Talk. Evonik, Darmstadt, April 2009
  • A. Arnold: “Accelerating Molecular Dynamics simulations using GPUs”, Invited talk, Seminar SFB 716, University of Stuttgart, Germany, May 2009
  • Marco Hülsmann: „Optimization of Force Field Parameters — Assessment of Numerical Algorithms“, Math. Oberseminar, TU Kaiserslautern, May 2009.
  • T. Köddermann: „Leitfähigkeit und "Ionenpaar-Bildung" in Ionischen Flüssigkeiten untersucht mittels Molekulardynamik Simulationen.“ Contributed Talk. Bunsen Conference, June 2009
  • Karl Kirschner: “Connecting Quantum Mechanics to Coarse-Grained Simulations: the Role of Force Field Development”, Warwick EPSRC Symposium: Workshop on Molecular Dynamics., Warwick University, England. June 2009
  • T. Köddermann: “Innovationen in F&E mittels Molekulardynamik-Simulationen” Invited Talk, Klüber Lubrication, Munich, July 2009
  • T. Brandes: “ESPResSo++: A Python-controlled, Parallel Simulation Software for Soft Matter Research” Contributed Talk. SciPy 8th Annual Python-in-Science Conference, August 2009
  • T. Köddermann: “Innovationen in F&E mittels Molekulardynamik-Simulationen” Invited Talk, Iolitec, Dietlingen, September 2009
  • Dirk Reith: “GROW: a GRadient-Based Optimization Workflow for Model Building Beyond Manual Intervention” Contributed Talk.„AIChE Annual Meeting 2009“, Nashville, TN, USA November 2009
  • Dirk Reith: “Atomistic and Mesoscale Modelling of Poly(methyl methacrylate) in Order to Understand Its Structural and Dynamical Properties” Contributed Talk.„AIChE Annual Meeting 2009“, Nashville, TN, USA November 2009
  • T. Köddermann: “Abschlussbericht: LogKow Ionischer Flüssigkeiten” Invited Talk, Klüber Lubrication, Munich, Dezember 2009
  • Karl N. Kirschner: "The art of Optimizing Atomistic Force Fields." Contributed talk given at HITS Mini Symposium, Heidelberg, February 2010
  • Dirk Reith: Contributed talk given at HITS Mini Symposium, Heidelberg, February 2010
  • Dirk Reith: ProcessNet, Multiscale Modelling… Wuerzburg, March 2010
  • T. Köddermann: “Investigating chemical compounds dissolved in ionic liquids” Invited Talk, Iolitec, Heilbronn, April 2010

Theses / Reports

  • Rawi, Reda: Comparison of atomistic and mesoscopic simulations in order to verify the coarse-graining procedure. FH Koblenz - RheinAhrCampus Remagen, 2007. Diploma Thesis
  • Brühl, Bernhard: Absatzprognosen für die Automobilindustrie in der Bundesrepublik Deutschland. Cologne University, 2008. Diploma Thesis
  • Heikamp, Kathrin: Atomistic Simulations for the Polymer Precursor Methyl Methacrylate (MMA). FH Koblenz - RheinAhrCampus Remagen, 2008. Bachelor Thesis
  • Aab, Tatjana and Nakhoumovich, Viktoria: Workflow-basierte Automatisierung chemischer Simulationen unter Berücksichtigung verschiedener Möglichkeiten der parallelen Ausführung. Universität Bonn, 2009. Diploma Thesis
  • Simeon, Petrus: Das Gram-Schmidt-Verfahren auf Graphikkarten. Universität Köln, 2009. Diploma Thesis

Mentoring

Mentee Type Time Period (Head-)Mentor

  • Reda Rawi Diploma Thesis Sept06 – Jul07 D. Reith
  • Timm Behner Pupil Internship Jan07 A. Maaß
  • Matthias Arbeiter Student Internship Feb07 – Mar07 D. Reith
  • Dominique Walter HiWi May07 – Dec07 D. Reith
  • Kathrin Heikamp Bachelor Thesis, HiWi Mar08 – Aug09 A. Maaß
  • Bernhard Brühl Diploma Thesis Sept07 – Jul08 D. Reith
  • Michael Volpers Masters Module Feb08 – Mar08 A. Maaß
  • Tatjana Aab Diploma Thesis Feb08 – May09 T. Brandes
  • Viktoria Nakhoumovich Diploma Thesis Feb08 – May09 T. Brandes
  • Andreas Bittracher Student Internship Jan09 – Mar09 K. Kirschner
  • Dorothee Ball Masters Module Aug09 – Sep09 A. Maaß
  • Jasmin Rubart Masters Module Aug09 – Sep09 K. Kirschner
  • Michael Lenz Masters Module Aug09 – Sep09 T. Köddermann
  • Petrus Simeon Diploma Thesis Nov08 – Dez09 A. Arnold
  • Olga Ivchenko Masters Student Jan09 - Mar10 K. Kirschner / A.Wolf
  • Farag Selim PhD Student Oct06 - A. Maaß
  • Marco Hülsmann PhD Student Apr08 - D. Reith
  • Antje Wolf PhD Student (Bio) Jan09 - K. Kirschner

Reviewer Activities

  • Carbohydrate Research (K. Kirschner)
  • Chemical Physics Letters (K. Kirschner)
  • Concurrency and Computation: Practice and Experience (T. Brandes)
  • Journal of Chemical Physics (A. Arnold, D. Reith)
  • Journal of Chemical Theory and Computation (K. Kirschner)
  • Journal of Computational Chemistry (D. Reith)
  • Journal of Molecular Graphics and Modelling (K. Kirschner)
  • Journal of Physical Chemistry (K. Kirschner, D. Reith)
  • Journal of Physical Organic Chemistry (K. Kirschner)
  • Macromolecules (D. Reith)
  • Molecular Simulation (D. Reith)
  • Physics Letters A (A. Arnold)
  • Physical Review E (A. Arnold)
  • R.E.D. Online Molecular Database (K. Kirschner)
  • Soft Materials (D. Reith)

Partner

  • Prof. Ludwig, Physikalische und theoretische Chemie, Rostock University
  • Dr. Sülzle und Dr. Hinrichs, Bayer Schering Pharma AG, Berlin
  • Dr. Grundei, Klüber Lubrication, München
  • Dr. Schubert, Iolitec, Heilbronn
  • Prof. Kurt Kremer, MPIP Mainz
  • Prof. Florian Müller-Plathe, Theoretical Physical Chemistry, Darmstadt University
  • Prof. Dr. Christian Holm und Prof. Axel Arnold, ICP, U. Stuttgart
  • Prof. Hans Hasse, U KL
  • Prof. Jadran Vrabec, U Paderborn
  • Prof. Roland Faller, Chemical Engineering and Material Science, University of California, Davis, U.S.A.
  • Dr. Johannes Vorholz, Evonik Darmstadt
  • Prof. Guiseppe Milano, U Salerno, Italy
  • Dr. Hans-Dieter Arndt und Prof. Herbert Waldmann, Max-Planck-Institute für molekulare Physiologie, Dortmund
  • Dr. Kurt Hoffmann und Prof. Rainer Fischer, Fraunhofer IME, Aachen
  • Dr. Marc Amkreutz, und Dr. Peter Schiffels, Fraunhofer IFAM, Bremen
  • Prof. Klaus Jurkschat, Technische Universität, Dortmund
  • Prof. George Shields, College of Science and Technology, Armstrong Atlantic State University, U.S.A.
  • Prof. Oliver Junge, TU München

Proposals

  • D. Reith et al.: MULTISCALE MODELING OF SOFT MATERIALS, NSF Partnerships for International Research and Education. Winter 2006/07. Role: Contributor. Status: – Rejected –
  • D. Reith et al.: ESPResSo: High-Performance Computing im Anwendungsbereich “Computational Physical Chemistry”. Summer 2007. MPG-FhG Program. Role: Coordinator. Status: – Accepted –
  • D. Reith et al.: Dynamic Coarse Graining of Proteins: Towards an Agent Based Description of Folding and Aggregation, NSF CDI-TYPE I, Winter 2007/08. Role: Contributor. Status: – Rejected –
  • Karl N. Kirschner: A Combined Computational Approach to Understanding the Ribosome's Resistance to Thiopeptide Antibiotics and the Design of New Lead Compounds. Fellowship proposal for VolkswagenStiftung. Summer 2008. Status: – Rejected –
  • A. Maaß et al.: Methodenentwicklung zur enzymatischen Funktionalisierung von Polymeren durch Modellierung des Systems aus Biopolymer-Lösungsmittel-Enzym. “Cluster Biopolymere” - BIOPRO Initiative des Landes Baden-Württemberg, Fall 2008, Role: Contributor. Status: – Rejected –
  • Thomas Brandes et al.: MAVO: MWare: Software-Technologien für die Zukunft. Fraunhofer: ITWM(Coordination), IAO, IESE, SCAI. November 2008. Role: Contributor. Status: – Accepted –
  • A. Arnold: Computer simulations to investigate crystal nucleation in suspensions of charged colloids under various conditions. Fellowship proposal within the DFG Emmy-Noether-Program, December 2008. Status: – Rejected –
  • Thomas Brandes et al.: PeaKlim: Petaflop-Architekturen in Klimaforschung und Meteorologie. Joint proposal of MPI-M and SCAI. Winter 2008/09. Role: Coordinator. Status: – Rejected –
  • Kirschner et al.: RNA-Proteintargets und Thiopeptidantibiotika: Modellierung in-silico und Chemische Biologie Das GTPase- Joint proposal of MPI-Dortmund and SCAI. Winter 2008/09. Role: Coordinator. Status: – Rejected –
  • Kirschner et al.: International Collaboration in Chemistry: High Accuracy Simulations of Glycolipids for Understanding of Cholera Toxin – Joint preproposal of UC-Davis and SCAI. Winter 2008/09. Role: Coordinator. Status: – Rejected –
  • A. Schüller et al.: BMBF project "Kongress zum Thema »Mathematik in der Praxis« im Rahmen des »Jahres der Mathematik 2008« und des Jahres der Wissenschaft 2009. January 2009. Role: Coordinator. Status: - Accepted -
  • A. Schüller et al.: BMBF project "Deutsch-chinesischer Kongress „Industrial Mathematics 2010", February 2009. Role: Contributor. Status: - Accepted –
  • D. Reith et al.: Integrale Strategien gegen neue Antibiotika-Resistenzen (ISAR). MAVO-Proposal (IME-IZI-SCAI), Spring 2009. Role: Coordinator. Status: – Rejected –
  • D. Reith et al.: Strategien für ein optimiertes Materialdesign von CFK-Verbundwerkstoffen durch wissensbasierte Materialentwicklung (SoMaC). MAVO-Proposal (IFAM-EMI-IZFP-SCAI), Spring 2009. Role: Contributor. Status: – Rejected –
  • Thomas Brandes et al.: SCICore: Integrated Scientific Simulations on Multi-Core Architectures, EU Proposal: P7-ICT-2009-4:* *Objective ICT-2009.3.6 Computing Systems. Spring 2009. Role: Coordinator. Status: – Rejected –
  • T. Köddermann et al.: „Kraftfeldentwicklung von Ionischen Flüssigkeiten mit Hilfe von MD-Simulationen" KMU-Akut Program, August 2009 Role: PI. Status: – Accepted –
  • D. Reith et al.: “Entwicklung eines Planungssystems für den Gebrauchtwagenmarkt und Wettbewerbsprognose”, ZIM Project Proposal, August 2009, Role: Coordinator. Status: – Rejected –
  • D. Reith et al.: Systematic Coarse-Graining of low-molecular weight organic compounds – Joint proposal for NSF-DFG-Grant of UC-Davis and SCAI. Fall 2009, Role: Coordinator. Status: – Rejected –
  • Reith/Kirschner et al.: Molecular Modulators. Joint proposal of MPI-Dortmund and SCAI. Winter 2008/09. Role: PI/Coordinator. Status: – Accepted –
  • T. Köddermann et al.: DFG Einzelantrag, tbd 2010: "Molecular Dynamics Force Field Development: Analysing the Force Field Parameter Space of Polarisable Molecules to Create Most Accurate Description of Reality" Role: PI. Status: – in preparation –
  • T. Köddermann et al.:"Technologien für Nachhaltigkeit und Klimaschutz – Chemische Prozesse und stoffliche Nutzung von CO2" BMBF proposal, tbd 2010, Role: Contributor. Status: – in preparation –
  • K. N. Kirschner et al.: International Collaboration in Chemistry: High Accuracy Simulations of Glycolipids for Understanding of Cholera Toxin – Joint preproposal of UC-Davis and SCAI. Role: Coordinator. Status: to be submitted in October to NiH (infectious diseases) or into HFSP, 2010
  • D. Reith et al.: Understanding of peptide folding dynamics for coarse graining purposes (Working Title) – Joint preproposal of UC-Davis and SCAI. Role: Coordinator. Status: – to be submitted in 2010 -
  • Köddermann/Arnold: Oberflächeneigenschaften von ILs
  • Arnold/Köddermann: Struktur von ILs in externen Feldern
  • HPC Ensemble Simulations (in preparation)


Ideas for new Proposals

Repetitive Calls: EU, BMBF, DFG, ZIM, US-NSF, US-DOE, US-NRH, HSFP, VolkswagenStiftung, …

EU-Partner: Pino Milano (IT), Detlef Hofmann (IT), Peter Ahlström (SWE), Doros Theoderou (GRE), Vagelis Harmandaris (GRE), Hendrik Meyer (F), Robert Woods (IRE)

IFAM – Airbus Polymers on Surfaces (Dirk)

Griebel – DFG ?! MD-CFD-Kopplung? Nanoröhren?....

FMP – BMBF Thema “Formulierungen” … (Dirk)

Kurt Kremer – Polymere aller Art …

Axel – Emmy-Noether Teile umformulieren und einreichen

Martin Hofmann/BIO – Neuro-Allianz, VPH-Initiative, …

C.Rümpler – BASF – Libosim-Connection (Dirk / Johannes)

Markus Deserno – Membranes…. (Dirk)

Jadran Vrabec – Optimierungsthemen (Marco / Dirk)

Hans Hasse – HPC, Opt, Phasendiagramme,… (Marco / Dirk)

GPU-MD (HPC-Topic) (Axel)

RNEMD Methods in GROMACS / Esp++ / … (Dirk)

Effective/fast/robust Equilibration of large Polymer (melt) systems (Karl/Astrid)

Effective/fast/robust Mapping and Back-Mapping AT – CG – Level (Dirk)

Breast Cancer: Derivatives of alpha-feto-protein / joint with BIO /Data mining ?! (Karl)

Atmospheric Chemistry – Chemical Pathways, Formation of small clusters, … (Karl)

MD-Tutorial(s) -- Itaca Money, BIT (Astrid)


Industrial Cooperations

Klueber Lubrications Status: - 1 contract completed (2009), 1 proposal and 1 contract planned (2010)

BDW Automotive Status: - 1 contract completed (2008), 1 proposal and 1 contract planned (2010)

Iolitec Status: - NDA signed, 1 proposal planned (2010)

CAM-D Status: - NDA signed, exchange of contacts, common marketing ideas –

GTT Aachen Status: - NDA signed, 1 proposal planned (2010)

Evonik Status: - Discussions about specific projects, no contracts yet

BASF Status: - Discussions about overlapping areas, no contracts yet

Bayer Schering Status: - Common search for third-party money / Contents of poss. work settled: Struktur-Dynamik-Beziehung von Röntgenkontrastmitteln in Wasser -


Organized Workshops, Seminars, Lectures, Teaching

  • Anton Schüller et al.: Seminar "Methoden der Computerchemie", University of Cologne, Summer 2006
  • Anton Schüller: "Große Gleichungssysteme - schnelle Lösung kein Problem", Fraunhofer Talent School München, November 2006
  • Dirk Reith: “Einführung in die statistische Mechanik”, Auxiliary Module Lecture, University of Applied Studies Koblenz-Remagen, RheinAhrCampus, Summer 2007
  • Anton Schüller: "Große Gleichungssysteme - schnelle Lösung kein Problem", Fraunhofer Talent School München, November 2007
  • Dirk Reith: “Mathematische Modellbildung und Simulation mechatronischer Systeme“, Auxiliary Module Lecture, University of Applied Studies Bonn-Rhein-Sieg, Sankt Augustin, Winter 2007/2008
  • Anton Schüller: "Große Gleichungssysteme - schnelle Lösung kein Problem", Fraunhofer Talent School München, March 2008
  • Axel Arnold et al.: Seminar "Numerische Simulation - GPUs", University of Cologne, Summer 2008
  • Anton Schüller: "Große Gleichungssysteme - schnelle Lösung kein Problem", Fraunhofer Talent School Bremen, October 2008
  • Dirk Reith: “Mathematische Modellbildung und Simulation mechatronischer Systeme“, Auxiliary Module Lecture, University of Applied Studies Bonn-Rhein-Sieg, Sankt Augustin, Winter 2008/2009
  • Anton Schüller and Ulrich Trottenberg: "Algorithmen versus Lösungsformeln - Lehreraus- und -weiterbildung". Workshop at the congress "Mathematik in der Praxis", Berlin, March 2009
  • A. Maaß, A. Arnold: “Wie entsteht eine Schneeflocke?”, SCAI, Girls' Day, April 2009
  • Dirk Reith: “Mathematische Modellbildung und Simulation mechatronischer Systeme“, Auxiliary Module Lecture, University of Applied Studies Bonn-Rhein-Sieg, Sankt Augustin, Summer 2009
  • T. Brandes, A. Arnold: “Anwendungen der Computerchemie”, SCAI, Schülerpraktikum, July 2009
  • Anton Schüller: "Große Gleichungssysteme - schnelle Lösung kein Problem", Fraunhofer Talent School Bremen, October 2009
  • Anton Schüller: "Große Gleichungssysteme - schnelle Lösung kein Problem ", Fraunhofer Talent School Birlinghoven, October 2009
  • A. Wolf and T. Köddermann: “Wie entsteht eine Schneeflocke?”, SCAI, Girls' Day, April 2010

ASTRID lectures !!!!

Software / Usage and „Products“


Sub-Atomistic

  • GAMESS (Usage only)
  • CPMD (Usage only)


Atomistic

  • GROMACS (Usage only)
  • AMBER (Usage and Co-Development of some Standard-FFs)
  • TREMOLO (Testing, Benchmarking)
  • TOWHEE (Usage only – should be abandoned soon – use ms2 instead)
  • MOSCITO (Usage of the analysis toolkit only)
  • Ms2 (Usage only)


Mesoscopic

  • ESPResSo++ (Core-Development)
  • LAMPPS (for Benchmarks, comparison to Esp++)
  • FORMULA1 (MFD) (Testing)


Tools and Toolkits

  • Desparo (Usage only)
  • ExAlto (Development inhouse)
  • CMA-ES (Marco, usage only)
  • Babel (Input-Conversion, Usage only)
  • RED (Calculation of partial atomic charges, Usage only)
  • Interoperability-Suite (Input-Preparation and Conversion, own Toolkit)
  • ELAN (Input Conversion, own Toolkit)
  • Analysis-Suite (Output-Data handling and Conversion, partly own Toolkit)
  • GROW (FF-Optimization Workflow, own Toolkit)
  • TRIANA (Workflow for automated simulation execution, own Toolkit)

Misc

  • Ibisco Meso-MD program by FMP – not used yet
  • Control-GUIs Griebel for TREMOLO, CAM-D for FORMULA1


Infrastructure

  • Force Field Database Astrid
  • Software Installations Thomas
  • Re-usable Transparencies Collector Thorsten
  • Article Data Base, technical issues N.N.
  • Article Data Base, Content Karl

Hardware Issues Thomas

  • Web Pages Content Toni
  • CoChE Library Dirk
  • Publication Tracking Dirk
  • Analysis Toolkit Marco
  • Interoperability Suite Astrid
  • Useful Web-/Wiki-Links Dirk

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“Know-How” – Guide?

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